During the bank heist before the school bus comes you see more than 6 bags full of cash, but only four bags being loaded onto the bus. Since the other bags were under the rubble and Joker was operating on a schedule (the opening between the school buses couldn't have been coincidence), he probably just left them.
When Alfred first meets Bruce Wayne in the "Batcave" they are talking. Bruce says, "That isn't exactly what I had in mind when I said I wanted to inspire people." The shot has already cut to another angle and Bruce's lips aren't moving, but he is still saying "inspire people."
In their final confrontation, when Batman struggles to get off the net, and the Joker tries to stab him with something, you hear the Joker's voice saying "All the old familiar places", but his lips never move.
When the school bus smashes through the wall during the bank heist, the goon that's supposed to get killed flies backward before the bus even gets near him, even thought there's a sound effect to suggest it hit him.
In the early vault scene, Lt. Gordon's speaking voice is also altered by mistake when he follows Batman, as Gordon says "we'd have to hit all the banks simultaneously, SWAT teams, backup": his voice is accidentally audio-"soured" as well.
When talking to Lucius about the cell phone surveillance device, Bruce says that "The database is null-key encrypted. Only one person can access it." In reality, null key encryption is an encryption scheme that doesn't change data at all, and is for when plaintext data is mandatory.
While planning to get into Hong Kong, Wayne says that he will use Korean smugglers who will fly under the radar the entire way there, and HALO jump out of the plane to get to the ground. HALO stands for High Altitude/Low Opening and the jumps are around 30,000 feet, well within radar range.
After the explosion at the warehouse, a fire hose is seen playing a jet of water from side to side across the top of the burning rubble. While this looks very pretty, a professional firefighter would never do this. They would concentrate the water at the base of the fire then work their way slowly across the blaze.
When Lucius Fox is showing Bruce Wayne the new Batman armor, Wayne picks up a wrist-guard with plates that are designed to separate at the press of a button. Wayne launches the plates by mistake, but when he places the wrist-guard back into place, the plates are still there.
As Batman interrogates the Joker, you can see that the amount of make-up on the Joker's forehead changes between the shots from almost fully covered to nearly disappeared (because of the slam on the table).
Two ferries are shown leaving Gotham just as the sun is going down. Later, it is established to be just shy of midnight, which would mean the ferries have been traveling for at least a few hours. Yet, the ferries are still shown as though they have just departed the harbor.
During the bank heist, one of The Joker's men grabs a security officer in the bank lobby, who is clearly wearing a white shirt. In the next scene when the bank manager shoots one of The Joker's men holding the security officer - the officer is wearing a blue shirt.
During the SWAT chase scene, the joker fires several rockets at the SWAT caravan. The final rocket is intercepted by the tumbler after it jumps over a car. In the shot where the tumbler gets hit, the SWAT truck is present and right next to the airborne tumbler. In the next shot when the tumbler hits the ground, the SWAT truck is not there.
In the scene that Bruce is taking care of the injury in his arm and Alfred starts to help him, he says:
"There were more copycats last night, Alfred, with guns." When he says that, he is looking straight, directly to Alfred. But when Alfred speaks, Bruce is already looking down. This happens several times during this scene.
When the Joker waves his pistol behind his head in order to shoot out the window before throwing Rachel through it, his pistol is pointed directly to the Joker's left, but the window directly behind him blows out when he pulls the trigger.
When the three robbers in the car (Grumpy, Chuckles, and Bozo/The Joker) enter the bank, Grumpy fires a shot in the air. Watch closely when Grumpy grabs a male teller saying "Let's go pal, I'm making a withdrawal here." In the background, Chuckles grabs the police officer standing near the entrance, drags him to a counter, and hits him in the back, which causes the cop to collapse. Apparently one hit to the back isn't enough, because just before the manager shoots Chuckles, the hit on the back is repeated.
When the Joker starts firing at the Batpod, he hits a Cadillac and it careens to the side of the street, taking down trash cans. Seconds later, the same Cadillac and trash cans are exactly as they were right before the Joker started firing at the Batpod.
In the scene where Alfred hands Bruce a glass of champagne, there are three glasses left on the tray from which Alfred serves. When the camera changes angles, there are four glasses visible as Alfred passes Bruce.
After The Joker tells the citizens of Gotham that he wants Mr. Reese dead in an hour or he will blow up a hospital, Bruce leaves to go to his Lamborghini. While Bruce crosses the room saying "I need you plugged in checking Gordon's men and their families," the TV in the background goes from showing a news broadcast to instantly being off as Bruce passes in front of it.
Before Batman jumps from the IFC2 skyscraper, he shoots a few timed explosives at the window of Lau's office, which is directly facing Batman. However when the windows explode, Batman and Lau were picked up by the sky-hook, and they are pulled out at the opposite side of the building. And now the IFC2 is behind them.
In the very first scene, the mirrored building has rows of rectangle and smaller square windows (one of which is a vent). In the exterior shot, a square window is blown out but when the camera switches to inside, it is clear the pair of thieves are in a room with the larger, rectangular windows.
During the chase scene when the tumbler collides with the garbage truck and immediately turns around, the road is completely empty. Not only should the armored truck be visible, but also the other cars which the truck must pass.
During the hospital scene where The Joker gives the gun to Harvey, you can see the heart monitor on Harvey's finger when he shows The Joker his coin. When the angle changes to The Joker's view, the monitor disappears, but reappears on his finger when the view changes back.
During the SWAT chase scene, the Joker fires several rockets at the SWAT caravan. The final rocket is intercepted by the tumbler after it jumps over a car. After the tumbler gets hit, it starts to flip. As it flips, it is clear that one wheel falls off. In the following shot, as the vehicle comes to rest, all four wheels are in tact.
When Joker is in custody they take away his jacket and gloves--when he's sitting in the holding cell clapping for Commissioner Gordon, when Gordon removes his handcuffs and when Batman is attacking him in the interrogation room, he has no gloves. But right after his escape when he's riding in the back of the police car, his jacket is still gone but he suddenly has gloves again.
After Batman hits The Joker a few times, The Joker is on the ground telling Batman about Harvey and Rachel. Batman grabs The Joker and when The Joker is talking to him, all of his teeth are yellow, except his bottom front teeth, which are bright and white.
In the SWAT truck chase, after The Joker fires a second missile from the tractor-trailer, the camera cuts to a wide shot of the vehicles and the "(S)LAUGHTER IS THE BEST MEDICINE" logo and artwork disappears completely from the big rig, leaving only a plain white trailer. It reappears in the next shot.
After toasting Harvey at the fund-raiser, Bruce steps out onto the balcony and tosses his drink over the railing. When the camera pans back, there is no liquid on the concrete ledge that extends a good few feet past the railing.
When Batman beats The Joker in the holding cell, The Joker's hands alternate between gripping Batman's arms from below, with the fingers pointing up, and holding Batman's arms from above, with his fingers pointing down.
In the scene where Batman jumps from the spiral parking lot ramp onto the Scarecrow's van, Batman is seen falling as the van appears to his left under him. He should land on the van facing its left side - but in the cut scene directly afterward he lands facing the same direction as the van.
When Dent is being transported in the SWAT van, the Joker shoots at the vehicle and you can see where the rounds have hit the armored car. However, after the Joker has been captured and Gordon opens the door to the armored car, there are no points of impact from the bullets on the vehicle's walls.
When the joker is asking for his phone call, he has the knife in his right hand with it up to the left side of Stephens's neck. In the next scene, however, Stephens has a bandage on the right side of his neck.
As the Joker completes his bank heist, he prepares to reveal his face to the bank manager by placing his right hand on his mask (his left hand can be seen holding the back of the manager's head). In the very next shot his left hand removes the mask instead.
Following the truck flip at the end of the car chase, the Joker approaches Batman, and 2 of his henchmen are visible: One who touches Batman's mask and gets electrocuted, and another who stands to the left of the screen, doing apparently nothing. This henchman disappears completely after Joker spits on the other, and is nowhere to be seen when Gordon arrives.
In the interrogation room, when Batman turns the lights on, the Joker puts up his hand to shield his face. It then cuts to a shot from behind the Joker and his hand is not there. Then in the next front shot of the Joker his hand is back where it was. Shortly after, the smudge of black makeup above the Joker's right eye gets larger between shots.
In the car scene at the beginning, the bank robber sitting at the back starts preparing his gun, while robbers at the front start chatting. When the camera turns to front angle, the robber is seen doing nothing.
In a scene where The Joker is telling Rachel the story of how he got the scars. The Joker's philtrum (a space between the nose and upper lip) is clean but in the dialogue "She can't stand the sight of me" you can see a blood or some sort of dark colored liquid on it. In the next frame it's gone.
When Batman jumps from the IFC2 skyscraper, you can see the Bank of China Tower to his right. When he crashes through the window into the building, you can see the same building again, but it's now directly behind him.
When The Joker confronts Rachel at the party and tells her about his wife, the angle at which he's holding his knife changes several times between shots - in one such change, he holds it against Rachel's cheek at a side-view, then has it under her nose immediately afterward during a close-up.
When Batman flies into the building, he knocks over the middle Hostage/Clown, but in the scene where he realizes the Clowns are hostages, the Hostage/Clown is back in the middle. This is most obvious when the snipers try to shoot at them, and you can clearly see all three of the Hostages/Clowns.
From the opening sequence to almost the end of the bank robbery, the Joker isn't wearing any kind of makeup, his hair color is natural too. After the scene of bus breaking in the mob bank, his hair change color to slimy green, revealing who he is.
At the beginning of the movie, during the heist, the robbers enter through the front doors (let's call this wall "north" and the wall that the bus crashes through is "west"). At the end of the robbery when the bus leaves and the camera shows the exterior of the bank, the bus makes a right turn (merges with the other buses which are running directly parallel with the front wall "north"). This is wrong since the bus only made a 90 degree turn, which would have made it directly perpendicular with the "north" wall instead of parallel as it is depicted in the film. In order for the bus to have merged with the other buses and proceed driving parallel with the "north" wall, it would have had to make a 180 degree turn instead of the 90 degree that was depicted in the film. You also know for a fact that the bus crashes through the "west" wall because throughout the heist, you can clearly see the windows that are shown later on the outside when the buses are leaving.
In the second segment of the Lamborghini chase scene, the car is heading south on Franklin Street. It passes Gene and Giorgetti's restaurant, which appears on the right at the corner of Illinois Avenue. Moments later, the car is heading north on the same street, and the crash occurs with the restaurant on the left side of the car. ( The restaurant has since been torn down.)
In the second segment of the Lamborghini chase scene, the car is heading south on Franklin Street. It passes Gene and Giorgetti's restaurant, which appears on the right at the corner of Illinois Avenue. Moments later, the car is heading north on the same street, and the crash occurs with the restaurant on the left side of the car.
When Bruce and Lucius are reconstructing the shattered bullet, the 3D image shows an entire thumbprint on the bullet. When the bullet was been pushed into the clip, the shell would still be in the casing, blocking the thumb partially from making a print on the shell. When the bullet had been reconstructed, it would have only been a partial print.
When Batman has the sonar vision on, he can see shadows of objects like the SWAT members and the Joker's dogs. Sonar would not pick up these shadows. While it is possible that the software which interprets the sonar data might create a virtual display with shadows for visibility's sake, that doesn't explain how the sonar manages to see the letters spelling SWAT on the officers' uniforms (e.g. in the scene where the SWATs exit the elevator).
For the hydraulic gun bender to work, it must apply superhuman force to both ends of the barrel; however, the device acts on the tip of the barrel only, while the impostor "batman" holds the other end of the gun.
It is said that all of the license plates seen on cars in the film are Illinois plates. In fact, they're not: if you look closely, they are actually plates for the fictional state of Gotham, although they resemble Illinois plates. The "Gotham" plates that were created by film makers were made to look like Illinois plates, just in case some slipped through in background shots during filming in Chicago.
Batman's voice has been criticized for being artificial-sounding and unnaturally gravelly. In the promotions for Batman Begins, the cowl is revealed to have a microphone/speaker that alters and amplifies Bruce Wayne's voice to disguise his identity and increase intimidation.
When Bruce, his date, Rachel, and Harvey meet in the restaurant, Bruce says he will "put two tables together." In the next shot, we see all four sitting around a single table. This wasn't meant to be taken literally, since he owned the restaurant his staff would have made sure that his guests were seated at a larger table.
The Joker claims he rigged the ferries with diesel fuel and ammonium nitrate and although diesel fuel normally only combusts under pressure and not with the addition of heat, ammonium nitrate/fuel oil (AN/FO) is a widely used explosive, even with diesel fuel.
When Alfred arrives at the shipping container yard he unlocks a padlock at the entrance to Batman's new lair. As this is the only (apparent) entrance to the lair - or at least the only one used in the film - an obvious question is how Bruce Wayne closed the padlock from the inside. However, the cargo door is clearly not large enough for a vehicle like Batman's tumbler, so at least a second entrance for the vehicle must be somewhere in the lair.
When Rachel is thrown out the window and Batman dives out to save her, we never see Batman go back up to his flat to flood out The Joker and his gang. However, with his trusty grapple hook, he could have done so in short time, and, having just received a vicious beating, The Joker's thugs were likely eager to get out of there. Simply because scenes aren't shown doesn't mean events didn't take place.
When we see the video of The Joker interrogating the fake Batman and he points the camera at himself, his teeth are really yellow and ugly. But when Bruce is watching the same video at his bunker, and the computer is analyzing the Joker's face, his teeth are all white and clean. However, The Joker's red painted smile appears to be black indicating that the image is in black and white.
When the Joker is talking on the loud speaker to the people on the boats, he says they have to press the button on the detonator. (The key is to prevent accidental button pressing. The button is still required to be pressed to detonate the explosive.)
During the interrogation scene when Gordon leaves the room and the lights come on, you can see the Joker close his eyes and brace himself to have his head slammed into the desk before Batman touches him. However, he was probably blinking from the bright lights coming on after he was in the dark for so long.
When they are trying to get Reese to safety, going into the alley and out of the building, you can see a cameraman running down the stairs after the police and Gordon. This cameraman is the one GCN reporter Mike Engle tells to follow him while he is reporting.
When he and Alfred are on the pleasure yacht, Bruce is picked up by a plane capable of water landings.
When he does the sky-hook to pick up Lau, the plane that retrieves him is a C-130 Commando Solo, incapable of water landings. Given that the first plane was there just to pick Bruce up and get him to Hong Kong via non-official means, there is no reason to suspect that its crew knew him to be Batman. Likewise, the crew of the plane that picks him up in the "sky-hook" operation would have no reason to suspect him to be Bruce Wayne, given that he's in his Batman outfit when they pick him up and he's not shown to reveal himself as Bruce.
When Jim Gordon puts a shotgun to The Joker's head after the street chase in Gotham, he is wearing a pair of glasses. Later when he opens the armored car door to let Harvey Dent out, he is wearing a different pair. Since it would have taken Gordon a minute or two to secure The Joker and his henchman, there's no reason he couldn't have also switched his glasses before opening the door.
The length of The Joker's hair changes throughout the course of the movie on several occasions. It begins mid length then changes to long, then back to short. This is suitable for this chameleon-like, disguise-loving character.
When the three members of the SWAT team rappel into the Prewitt Building near the end, you can hear their sub machine guns fire at the windows and clearly see all three windows crack under the gunfire, however, if you look closely only one of the guns give off a muzzle flash. This is not a mistake, guns do not always flash when fired.
From the timeline in the film, it appears that Gordon and Batman investigate the opening bank heist after Batman busts a meeting between Scarecrow and the Chechen. However, it is more likely that the bust occurs a day after the bank heist. For one, it is late when Gordon waits at the bat-signal ("Ever intending to see your wife again, lieutenant?"), yet it's only dusk when he enters the bank. It's unlikely that a crime scene would sit for so long before Gordon investigated it. Also, Gotham Tonight's episode 6 ends with reports of the bank heist taking place, although episode 7 is aired in the film right "after" the bank heist but immediately before Batman's introduction in the Scarecrow-Chechen meeting. Batman's elbow is also not visible when he speaks with Gordon, so it is possible that he hadn't been bitten by the dog at that time, and thus hadn't faced the Chechen nor his dogs.
During the bank heist, the Joker puts the smoke grenade in the bank manager's mouth. The bank manager does not know at this point it is only a smoke grenade. The Joker then jumps into the bus, closes the door, gets in the driver's seat and drives the bus away. During this entire time, even though the bank manager has use of both arms and is not tied up, he leaves the grenade in his mouth, when he could have easily removed it and thrown it towards the bus as to not have the string pulled.
The Joker takes the detective hostage inside the squad room and asks to make a phone call. At the same time, the unconscious prisoner in the holding cell nearby is found to have something surgically inserted in his body. The detective tosses his cell phone to the Joker and he dials. We see the item inside the prisoner's body light up and there's an explosion. The blast force is strong enough to shake the squad room, but all we see is papers flying around the Joker as the camera is shaking. The Joker is fine, still standing. The detectives, including the Joker's hostage, have suddenly disappeared. The blast did not affect the Joker. Where did the detectives go?
In the part where all the crime leaders are having the meeting with Lou live on TV, the TV screen gives off a green reflection on the table which means that they put a green sheet over the TV screen so that can put over another version (special effects) of the live video of Lou.
In the opening bank heist scene, the Joker inserts a grenade to the mouth of the manager lying on the floor. A string from the pin of the grenade is attached to Joker's clothes, and once he leaves the bank by the bus, the pin of the grenade is seen to fall off to the floor, as expected. However the pin does not move after that, even though it is now attached to a bus that is speeding away from the location, suggesting that it should disappear from the screen rapidly.
Many cameras were used to shoot the scene where Wayne's Lamborghini blocks the pickup from ramming the SUV carrying Gordon. CGI was used to remove them in post. However, the IMAX cam that was on the chase vehicle actually hit the bed of the pickup. In the overhead shot, watch the pickup's stake pocket behind the driver's door. The dent from the camera strike suddenly appears even though the camera has been removed.
Green screen reflection: When the Joker slams the pencil onto the table, you can clearly see the green reflection of the original television screen on Gambol's table. Although the screen has been digitally replaced later with a shot of Lau, the green spill remains.
During the chase scene on the lower street level the truck in which the Joker is riding hits the right side of the SWAT truck, however the SWAT truck flies off into the river as though it had been hit on its left side. Furthermore the road changes from a gradual right turn immediately to a gradual left turn. In the special features the original shots of the SWAT truck going into the river reveal that it was correctly shot such that the truck appears to be hit from the right side but the film was simply reversed.
Gordon shuts the heavy iron door as he walks into the interrogation cell to question The Joker. The reflection in the mirror shows the door swinging open again. That means the door was unlocked, and it's much lighter than it looks.
During the bank heist, the manager's shotgun is single-shot, meaning he must cock the gun before each shot. He shoots at the Joker right after shouting "Hey!" However, before this shot, he is neither seen nor heard cocking the gun. Also, between the gunshot before this one and when he shouts, there is almost no time slot in which he could have cocked the gun.
When The Joker gets into the vehicle on the way to the bank heist, he produces a modified Glock 17 and a magazine. When he inserts the magazine into the weapon and pulls back the slide to load it, the slide locks back and he has to depress the slide release to let the slide cycle forward. This means the magazine is empty, as the slide would cycle forward instead of locking if the magazine had been loaded.
As Joker and Batman (on his Batpod) face off, a banner on the building behind Joker reads "Sweet Home Chicago" - the actual location where the downtown scene was shot. (A line below the name reads "Chocolates - Nuts - Coffee - Pastries," indicating that it is a local store with a pun in its name, not travel or event-related.) A short distance away, when the armored transport carrying Harvey Dent stops, a LaSalle Street address can be seen, indicating the street the shot was filmed on.
The goof items below may give away important plot points.
When Two-Face hangs up on Commissioner Gordon, a standard telephony off-hook signal can be heard on Gordon's cell phone. This is a signal used in standard land-line telephone exchanges and would not be applicable on a wireless phone network, which works differently.
When Bruce Wayne is riding his motorcycle underneath an 'L' line while racing to the apartment overlooking Commissioner Loeb's funeral, he passes a modern Volkswagen New Beetle. The sound of the car is that of an old, 4-cylinder boxer air-cooled beetle, and not the sound of a Volkswagen New Beetle.
During the opening bank heist, the bank manager shoots Grumpy in the shoulder (before Bozo/The Joker guns the manager down). In later scenes, however, there is no visible injury and while loading the cash, Grumpy does not seem to be hindered by his wound.
At the end of the long trailer chase scene, when The Joker confronts Batman in the Batpod. When he fires a second round of shots from his submachine gun, the Batpod is clearly visible next to the car he is shooting at. Then in the next take the Batpod is in the same location.
In the hospital, when The Joker places the gun in Two-Face's hand and points it at his own head, he cocks the hammer. When the camera faces Two-Face, The Joker's finger is over the hammer. When it's facing The Joker, it's not there.
After The Joker blows up the hospital and sits down on his bus, a crew member in the very last row wearing white headphones or ear muffs can be seen closing the Emergency Door on the bus then appears to cue the bus driver. Immediately after this, you can see him ducking down so as not to be seen.
As the bus is driving away after The Joker blows up the hospital, you can see an IMAX camera in the seat opposite of him. This was to film a shot on the bus that was deleted (as explained in the special features).
When Harvey Dent has had half his face burned off, his lips on his left side are gone, leaving his teeth, cheek muscles and tendons exposed, however, his speech remains almost exactly the same; in real-life, he would be nearly-impossible to understand. His exposed left eye should be useless as well, yet he is able to move it and see out of it.
When disguised as the honor guard at Loeb's funeral, during their attempt to kill the Mayor, the Joker and his men use M1 Garand rifles to carry out the three volley salute. Since funeral procession guns are blank converted or fitted with blank adapters (they could lack both but these guns clearly fire as semi-automatics), the guns are either following the movie myth that blanks and live rounds both work in live guns, or they removed the adapters and are firing live rounds into the air for the first two volleys.
When Two-Face is in the hospital which The Joker plans on blowing up, you can see make-up on his pillow which has rubbed off from the "burnt" side of his face. Actually the burnt part of his side is completely CGI, and the "make-up" is supposed to be "ashes" or pieces of Two-Face's burnt side rubbing off onto the pillow.
Harvey Dent confesses to being Batman yet nobody seems to notice his chin dimple - something which Dent clearly has but Batman clearly doesn't. However, very few people have actually seen Batman in person, since he largely stays hidden in shadows and only reveals himself when fighting bad guys or talking to police, so this is a detail that most people would not be familiar with.
When Maroni arrives at the hospital and confronts Gordon he is standing. But Batman "interrogated" Maroni and threw him off a building where he landed on his feet. However, he only injured one ankle. Several scenes after the fall he is shown carrying a cane indicating that only his one foot is injured and he can walk fine with just a cane.
When Lucius Fox asks Bruce about the new military cellphone division of the company, Bruce says, "I'm playing this one pretty close to the chest." However, after the capture of the Joker, Gordon lets Dent out of the back of the SWAT van, and Dent says, "You DO like to play things close to the chest." Suggesting that Gordon had said it before his staged death.
Harvey Dent is soaked in gasoline on his left side, the heat and flames of the ignition are enough to burn off the entire side of his face, down to the bone in some areas, yet his suit remains completely intact, with some minor burns to the shoulder area.
Near the very end of the film when Batman is telling Commissioner Gordon to blame Two-Face's murders on him, the film cuts to a dead Two-Face lying on the ground. For the brief moment the shot is on Two-Face, you see just the prosthetic on the actor's face and not the CGI-enhanced version in the rest of the film.
When Salvatore Maroni gets into the backseat of his car towards the end of the movie, as soon as the door is shut by his henchman and he is startled to discover Dent waiting for him, the view out of Dent's window shows the car traveling at highway speed rather than just beginning to accelerate from a stop.
When Commissioner Loeb is choking on the acid he drank, the camera cuts to the acid burning a hole in Loeb's desk. However, there is also liquid quite obviously on the keyboard by the cup and smoking hole and it is not smoking.
Gotham General Hospital is the administration building for the old Brach's Candy Factory in Chicago (and in fact, if you look closely in the aerial view of the hospital imploding, you can see the Rock Island District tracks and the South Side 'L' tracks). When the building is going up in flames, and the aerial shot swings around to the one side, you can see that windows in the back are different, and the interior is gutted. The windows in the upper floors were added later in post-production, since it was explained in the special features that the windows were stolen from the production site before they could be installed.