When Spider-Man "steals" his costume back from J. Jonah Jameson, Jameson is heard yelling "he's a thief, a criminal" etc., however, in the shot where Jameson is standing next to the web/note left by Spider-Man, his mouth is not moving.
When Octavius introduces his four arms, and as he turns to have the device attached to his back he says, "They are impervious to heat and magnetism." As he turns his lips are not moving but we hear him speaking.
In the first battle scene with Doc Ock fighting Spider-Man, Spider-Man, who has strength proportionate to a spider, hits Ock plenty of times, not only with his fists, webs, and feet, but with a desk and a window, too. All of these times Ock barely flinches with the blows. And yet, at the end of this scene, the elderly Aunt May clubs Ock over the head with an umbrella hard enough not only to make him back off but to break his sun glasses which were previously unscratched.
When Peter jumps across the table to save Mary Jane from the car coming through the window, her chair falls over as he grabs her. In the next shot we see him lift her out of her chair without toppling it.
When Dr. Ock walks out of the hospital and flips the taxi that's coming toward him, the oncoming traffic changes between shots. You can see that the car is going to land on its hood in the middle of the street and there are no cars parked, yet in the next close-up shot, it lands on its wheels and over a parked taxi, pointed on the wrong way.
When Henry (the little boy helping Aunt May pack) says, "Hi" to Peter, he is standing by the driveway, yet in the next shot when Peter tells him "You're getting tall", they both are standing several feet away, right in front of the garage door. The same switch takes place when Aunt May tells Peter "Everybody loves a hero".
When Spider-Man is trying to stop the train, the font left window of the first car shatter, we can see that the handrails are on each side of the door, (pointing toward each other). The next shot shows the suit on his left arm ripping, and then the handrails are now pointing forward. A couple of shots later, when the right window shatters, the handrails are again pointing toward each other.
When Peter Parker arrives at the theater playhouse to see Mary Jane's play, he is driving the car of the criminals whom he had just bagged as Spider-man. In the first wide shot, the car's windshield is intact. However, the subsequent shots show the windshield ripped off at its base. This is because the preceding chase sequence originally included the car driving underneath a semi-truck, but once that part was cut, CGI artists went in and replaced the windshield for the establishing shot.
When Dr. Ock and Spider Man are fighting and fall on the passing train, they start rolling, leaving huge dents on the top of the first car, as seen by the passengers inside, yet in the next shot the train appears undamaged.
When Spider-Man saves Mary Jane and has her suspended in a web on the crane, the first shot shows her on the very edge of the right-hand side. In the following close-up shots you can see plenty of web to her right, making it look like she is in the center.
At Joe's Pizza in the beginning of the film, as Mr. Aziz is speaking with Peter, a man sitting at a table behind Peter is drinking from a cup labeled Dr. Pepper. In the next shot, the man has an empty 20 oz. Dr. Pepper bottle next to his cup which subsequently disappears again.
When Aunt May is moving her things out of the house and Peter comes over, she gives him a hug. The first shot shows Aunt May's head resting on Peter's right shoulder, but in the next shot, Aunt May is resting on Peter's left shoulder.
When Aunt May is outside her house packing her things into boxes with Henry Jackson, she hugged Peter after saying 'I love you, Peter.' When she first hugged him, her head was to Peter's left shoulder. But when the view changes, she has her head to Peter's right shoulder. When the view changes again, her head is back to Peter's left shoulder.
As Peter is walking along the top of the building, about to do his "I'm back" jump, he is about three quarters of the way past a skylight on the roof. Then the shot changes, and he is just walking up to it.
When Peter is first seen running with the pizzas, he is carrying eight boxes. In the next shot he is carrying seven, and Spider-Man only leaves seven on the balcony. When Peter delivers them, there are once again eight boxes (two have been crushed together, but this does not account for the changing number of boxes).
When Peter makes his pizza delivery the clock behind the woman's desk shows it to be about 2:06. When Peter gets to her desk a few seconds later to drop off the pizzas, the woman looks at the clock on the wall and the time is 2:03.
After Spider-Man loses his powers for the first time, he falls in a puddle which soaks his hair and leaves one part of it sticking up. As soon as he attempts to climb the wall, though, his hair is not only slightly wet but it is perfectly combed.
After fighting outside of the bank, Doc Ock is carrying no money bags. There are many shots showing all his free hands and even when they leave the bank initially there is nothing in his hands. Then when we see Doc Ock leaving there are two money bags in his tentacle.
In the pizzeria when Peter is being fired, there are words at the top and bottom of the clock behind him. Halfway through the scene, there are only words above the clock. The words at the bottom are gone.
In the "Horror Hospital" scene, Dr. Octavius is prone on the operating table with his head supported by a Mayfield horseshoe in all shots except the one from underneath the table looking up at his face where his head is held in place by a Mayfield skull clamp (a.k.a "Crown of Thorns").
When Otto Octavius is demonstrating the fusion experiment to the group, Peter Parker is standing right next to Harry. In another shot, Harry is by himself. In the next one, Peter is back next to Harry.
When Dock Ock is climbing the building right after the bank heist, we see from inside the offices how the tentacles crash though the wall - the pincers are closed in their "spiky" form and penetrate the wall completely. However, when the view changes to outside we see the pincers open and "grabbing" into the masonry, not going through the wall but only into it enough to hold on.
When the film begins to play the "Raindrop Keep Fallin' On My Head" song, the viewer could see that Peter is walking in Central Park and then proceeds to fall. When he gets up however, you see him standing on a busy street.
When Peter and MJ are sitting int he café, there a lot of people around. When Doc Ock throws the car, there is no one as the car lands, but then when Doc Ock, enters the café, there a lot of people around.
When Peter and MJ are walking together after Peter goes to see MJ's play they stop to talk to one another at the end of the street. In this shot there is no car behind MJ but the next camera shot facing her shows a taxi in the background behind her which she later gets into.
When Spider-man is fighting Doc Ock for the first time in the bank behind Doc Ock are the windows of the bank that he will crash into later. When you look in the windows you see a White bus with a orange line in the middle that says "Metro Bus", a Los Angeles company.
There are no elevated trains in Manhattan running near skyscrapers or between high-rise buildings. The longer shots of the train exterior look rather like Chicago "L" lines, and in fact, the 'making of' reveals this footage was shot in Chicago.
Even though the runaway train is shown to be an 'R' service, which is headed for Bay Ridge - 95th Street (in Brooklyn), it is never shown how the fictional elevated line gets to Brooklyn so that the service could join the real life BMT Fourth Avenue Line. The line dead-ends in Manhattan, and never gets to cross the East River.
When Peter tries his "I'm back" jump, he is moving in a parabolic curve until his jump fails and he drops straight down into the alley. Physics states that he would have continued on his parabola, causing him to hit the wall at some point.
During the car chase, the criminal in the passenger seat first fires a shotgun at the police, and then when he notices Spider-Man, he pumps the action, but begins to fire some form of fully automatic weapon (a shotgun is not an automatic). In the next shot of the car, he is still holding the shotgun, but continues to fire it like an automatic.
When Doctor Octopus exits the hospital, two of his mechanical arms pick up and throw a taxi, while the other two brace themselves on the street. But in the scene where he rips off the bank vault's door, he uses all four arms. This would be impossible unless his biological legs and back had the strength to lift the vault door.
The runaway train is shown to be an 'R' train, and is shown to have blinker doors. In the real subway system, the 'R' is unique in that it is totally underground, except for a short stretch in Brooklyn when it crosses the LIRR Bay Ridge Branch. Also, the 'R' uses R46 subway cars (and some R160s), both of which have sliding doors instead of blinker doors.
In the train fight sequence, the train says Bay Ridge in the destination window on the front of the train. On real subway cars, there are no destination signs on the cab ends of the cars: only a letter or number rollsign or LED display is present. The only destination signs in the trains are on the sides of the cars. Historically, however, there has been New York City Subway rolling stock that has been equipped with end destination signs (like the Redbird trains used on the IRT until 2003, and the R32 and R38 cars prior to being retrofitted with flipdot signs in the 1990s). Despite this, no rolling stock has been built for the subway with blinker doors. All stock has been constructed with sliding doors. However, this is a fictional route created for the movie (see Trivia), and it might not necessarily be tied in with the real subway system.
Parts of the lower side of the construction in which Doc Ock has set up his second experiment are also made of metal. This means that when the experiment fails again, the base of the building would be sucked into the tritium sphere as well. This in turn would cause the structure to collapse so that the sphere would fall into the river.
After the cemetery scene and before Peter confesses about Uncle Ben, there is an establishing shot of Aunt May's house. The way her yellow car is parked in the driveway leaves no way for the doors to open. The space between her house and MJ's parents' house is too narrow. Obviously the car was rolled in to obtain the shot.
Obvious pre-rigging of Spider-Man's costume in the trashcan, presumably to match the famous comic book image of the same scene, which indicates it's a different one than in his hands. He then drops straight down which means it'd miss the can since the can is several feet to the side!
In the scene when Spider-man is about to fall off the mono-rail, but the passengers grab him, you can clearly see his muscles flatten underneath the hands. This makes it obvious he is wearing a muscle suit.
In the burning building scene, after Peter misses the jump and he's hanging over the fire, he throws the little girl onto the ledge to save her. A dummy is obviously used because of how hard she was slammed against the floor and how she doesn't react to the slam.
In the zoomed-out shot of Spider-Man stopping the train, he's not holding onto the webs, nor are they anywhere to be seen. In all immediately-previous and immediately-subsequent shots, they are clearly visible.
When Peter Parker saves the child from the burning building, she is old enough to stand and help him up. However, when he hands the child to the parents after exiting the building, the fake bundle he hands them is the size of the infant.
When Peter runs down the alley to change in to Spider-Man, his costume has a low neckline to hide beneath his shirt. When he removes the mask after falling on to the rooftop the neckline is higher, indicating that it is a different costume.
When Peter is untying the ropes holding the pizza delivery together at the secretary's counter, near the end of the shot you can see the secretary holding up a bottle of water with a straw in it, and drinking out of it. However, the straw never touches the water.
Peter's powers return indefinitely after Doc Ock kidnaps Mary Jane. Peter notices this because he no longer needs his glasses. The shots from his POV change between clear and blurry, glasses off or on respectively. When the shots are blurry, the audio is ramped down.
When Dr. Octavius's experiment goes awry and the reactor begins pulling all metal objects into itself, a close-up of his wife shows that her dangling earrings are still swinging freely as she moves her head.
The goof items below may give away important plot points.
When Harry Osborn is preparing to confront Spider-man he picks up a large sheathed dagger. As he does this, the sound effect is of a blade being unsheathed. We hear the same sound effect a second time when Harry actually unsheathes the dagger just before unmasking Spider-man.
Near the end of the movie, in the scene where Doctor Octavius starts his second fusion experiment, Spider-Man pulls out the plugs to stop the machine. But a few camera shots later when Spider-Man takes off his mask in front of Octavius, you can see the plugs behind him perfectly intact.
Spider-Man's right eye-piece is burned during his fight with Dr. Octopus on the train, necessitating its removal. When the mask is returned to Spider-Man, the burned eye-piece is clearly visible. However, when Dr. Octopus delivers a bound and unconscious Spider-Man to Harry Osborn in the next scene, Spider-man's mask is undamaged.
The scene after Spider-man defeats Doc Ock, he and Mary Jane are talking on a giant web. When the camera is on Peter's face, look at the webbing behind him, you can easily see through the clear web-like matter and see the metal wires that make up the web.
After Doc Ock kidnaps MJ he takes her back to his lab and has got her tied up behind him while he works on his machine. Her arms are almost vertical and straight in the close-ups but she has bent elbows in the long shots.
Doc Ock was told to search for Peter Parker for information on the location of Spider-man. When Doc Ock notices him at a café, he introduces himself by throwing a car through the window. If he thought Peter was a regular person, why did the throw the car at him?
Flipped shot: Near the end of the film, while Peter Parker/Spider-Man is on top of the large crane, he is in a prone position; and we see a rip in his outfit along the top part of his left thigh. Moments later, the camera re-cuts back to him, and the rip is now on his right thigh.
In the warehouse, during the climax of the movie, when Spider-Man is on the ground and Dr. Octavius grabs him, there is a chain on the ground next to Ock's legs. Ock's machine is supposed to attract metal. However, the chain is not being attracted at all.