Before the fight inside the elevator begins, Captain America asks, "Before we get started, does anyone wanna get out?", if you look at the words he's mouthing, he clearly says the word "off" instead of "out".
After Fury arrives at the Triskelion via helicopter during the final battle, he confronts Pierce and asks, "Why make me head of SHIELD?" to which Pierce replies, "Because you're the best." While Pierce is seen from behind as he says this, it can be seen that his mouth movements don't match this line.
When Pierce activates the badges being worn by Natasha and the S.H.I.E.L.D. Councilmen, he threatens to burn a two-inch hole in Natasha's sternum. The sternum, aka the breastbone, is in the center of the chest, while the badges are on the wearers' right sides, over the rib cage.
(at around 1h 14 mins) Falcon takes Jasper Sitwell hostage in front of the restaurant. Falcon says, "There's a gray car two spaces down. You and I are going to take a ride." After the rooftop interrogation, during the chase on the overpass, Falcon's car is black.
When showing Rogers the three new Helicarriers, Fury tells him 'After New York I convinced the World Security Council we needed a quantum surge in threat analysis.' The word 'quantum' refers to the smallest possible amount of something, so Fury is saying that he convinced the WSC to make the smallest possible increase in threat analysis - however, what he shows is a huge change.
Batroc is said to be French-Algerian. However, he has a very distinctive French Canadian accent, nowhere near any accents commonly heard in France or the Maghreb (Think of it as like an Australian actor sticking to his native accent while portraying an American character)
When Cap and Widow enter Zola's computer room, it is after having descended several levels below the bunker using a hidden elevator. After the missile strike, they are shown to be only a few feet below ground level.
In the opening scene of the movie, when Captain America sky dives on to the deck of the ship along with the rest of his team, there is a huge storm at sea with high winds and large waves in the ocean. When they land on the deck of the ship, the air is so calm that their hair doesn't even move.
The Triskelion is located on Theodore Roosevelt Island - in the opening scene, as Steve and Sam are jogging, the Triskelion is tall enough that it should have been visible to the north of the Abraham Lincoln Memorial, yet it doesn't make an appearance.
When Captain Rogers gets on the elevator with Nick Fury, the computer identifies him as being a Level 8 agent. Later in the film though, Alexander Pierce refers to Rogers and Romanoff as being Level 6 agents. The latter seems accurate as Agents of S.H.I.E.L.D. establishes Phil Coulson as Level 7, and in The Avengers and Thor, he can be seen giving orders to Romanoff and Clint Barton.
When the hovercarrier collides with the Triskelion, Romanoff is seen running to escape the collapsing building still wearing the outfit she wore while she was impersonating Councilwoman Hawley. However, a few seconds later, after she is in the helicopter, she is suddenly back in her signature black leather jumpsuit.
When Steve returns to the hospital vending machine for the flash drive, the gum and drive are missing. Natasha appears behind him chewing gum. When he pushes her in the other room to talk she no longer has gum in her mouth.
During the police attack, Fury's SUV is able to get away because of the significant space left by the rear vehicle but only seconds before, it was nearly under the SUV. Fury's AI accelerates forward but doesn't move the front vehicle either. We can see this because the battering ram is still next to the driver side window.
When Sitwell is confronted by the Falcon at the cafe he has a Hydra pin on his left jacket lapel. In the next scene while he is talking to the Captain and Black Widow on the rooftop it disappears. After he is thrown off and caught by the Falcon and thrown back on the rooftop it magically reappears.
When Natasha and Steve are at the Apple Store, Natasha plugs in the pen drive onto the left hand side of the MacBook but when the S.H.I.E.L.D members arrive, the pen drive is missing from the USB port and then again in the next scene it comes back.
(at around 1h 16 mins) At the start of the bridge fight, Winter Soldier is shown in carrying a few knives on his belt and holster. When he is first seen being thrown off the car, landing on the asphalt and shooting, he is shown carrying a mid-size combat knife on his right leg rig. The knife is correctly shown as being a Cold Steel GI Tanto (Model 80PGTK). At about 1h 22m 30-31s, a few minutes into the fight, as Rogers is running toward him, he draws a completely different knife from the same sheath, this one being a current generation Gerber Mark 2 combat dagger (Model 22-01874).
During the highway car chase, the car that Steve, Natasha, and Falcon are in scrapes another car on their left side, resulting in the driver's side rear-view mirror breaking off. However, in the next full shot of the car, the mirror is seen perfectly intact.
(at around 1h 35 mins) When Steve is addressing the Triskelion from the control room before the helicarrier launch, he briefly wears his shield on his back using the same brown harness that he used to wear the shield with his "stealth suit" earlier in the movie. However, at this time he was wearing his World War II era costume with a harness already attached, so he would not have needed the brown harness to carry the shield on his back. Shots immediately before this scene (such as when he, Sam, and Maria approach the Triskelion through the woods or when they enter from the stairwell into the control room) do not show Steve wearing the brown shield harness.
In the New Jersey secret bunker scene, Zola explicitly mentions that S.H.I.E.L.D. was founded after World War II. However in Iron Man Agent Coulson introduce himself to Potts as being part of the "Strategic Homeland Intervention, Enforcement and Logistics Division" - implicitly saying that the acronym S.H.I.E.L.D. is not yet in used, because "they" haven't figured it out yet ("it's quite the mouthful?" "yes, we're working on it")
How come Zola, dead way before the Iron Man era, knows about the S.H.I.E.L.D. acronym ?
When Nick Fury pulls up to the stop light and the police car pulls up next to him, the long shot shows the passenger side window of Fury's SUV to be closed. The close-up when the cops are looking at Fury and Fury's response shows the window to be down when Fury asks if they want to see any paperwork. Then when it goes back to the wide shot/long shot, the window is once again closed.
From the time Captain went to hospital to gather USB to the time they exit mall and borrowed a car to go to New Jersey, Captain was all in disguise and Captain was not carrying his shield. Also when they exit the car in New Jersey Captain was still without his shield but when they came to the door to the secret elevator, his shield suddenly appeared in his hand to break the lock.
(At around 6:17) When Steve and the SHIELD Strike team are assaulting the Lumerian Star, Steve is running along the starboard deck of the ship. He enters a tunnel or corridor and is hidden from view for a second. After this hidden interval, he emerges from the corridor in about half the time that he should have, judging by his running speed. This can easily be seen by slowing down the video to half speed.
When Hydra soldiers underneath the bridge are shooting at Captain America right after he gets out of the crashed bus we see bullet shells pile up at the feet of one of the soldiers on the car he is standing on, however when Captain America attacks the soldier the bullets are gone.
When Falcon and Rumlow are fighting in the Triskelion, after Rumlow throws Falcon through a glass desk partition, he jumps up on the desk, and we see blue skies outside the windows behind him. In the very next shot of him, the final Helicarrier shows up immediately outside the window, despite not moving at such a speed.
When Cap and Falcon are running to attack the helicarriers ("How do we know who the bad guys are?"), Falcon spreads his wings to take off and Cap is inside the wingspan. On the next overhead long shot, Cap is well to the right of Falcon's wingtip.
In an early scene the location is given as "Indian Ocean Lat 16N 55' 12.06" Long: 72N 56' 7.09" " Longitude represents E/W, so the 72N should be 72E. That would put the plane just off the coast of Ratnagiri, India.
When Steve and Natasha enter New Jersey, they are clearly driving across a landlocked border. Since they were driving North from Washington, DC, they would have entered into New Jersey from Pennsylvania or Delaware. Both states are only accessible to New Jersey by crossing the Delaware River. New Jersey's only landlocked border is on the Northernmost region of the state, crossing out of and into New York State.
The first time we are introduced to the Triskelion S.H.I.E.L.D. HQ building, the latitude/longitude are given as "38N 53'33.78" 77S 3' 38.91". Longitude is given in 'E' or 'W' (East or West), not 'S' (South); in this case it's to the west, locating the Triskelion on Theodore Roosevelt Island in the Potomac River, Washington DC, USA.
During the chase scene, Fury's navigation system tells him that 17th Avenue is clear up ahead. There is no 17th Avenue in DC, the navigation system should have said 17th Street (SW if it was being truly accurate as Fury was shown driving by L'Enfant Plaza and going toward the Roosevelt Bridge).
In the bunker with the computer equipment from the 1970s, the top and bottom reels of the tape drives moved in steady unison. Unless every tape was exactly at the middle, the reels would have to spin at different speeds. But they didn't work that way anyway; vertical tape drives of that period were "vacuum column" drives. They were very jumpy (lots of starts/stops) and the top and bottom reels were staggered in motion (one speeding up slightly before the other).
During the Zola scene, the computer monitors show news headlines and stories that elaborate on past events Zola tells our heroes about. But these are "black and green" monochrome computer monitors; they would not have been able to produce full colored images like this, let alone with the crisp HD quality they are presented in.
When Captain America is escaping from SHIELD on his motorcycle and confronted by the hover-jet, he is seen slaloming to avoid the strafing from the mini-gun. However, the mini-gun fires a stream of bullets, and he would have had to drive through them to do that.
When Steve Rogers and Natasha Romanoff are driving the Chevrolet pickup truck to New Jersey, the shifter handle is visible next to the steering wheel when the camera pans to Rogers who was driving. The shifter handle should not be visible if the truck is truly in Drive as it was portrayed.
Captain's shield during the opening ship scene has a different color scheme. To be more specific it lacks red. If the shield is paid attention when it is close to white light sources where flesh tone is neutral, red still can't be seen on the shield. As further proof, in scenes where Black Widow's red hair -which is relatively pale compared to shield's bright red) can be clearly seen as red, shield is still in shades of blue.
The movie makes numerous references to Black Widow (born in 1984) being part of the KGB, which folded in 1991. She would have been about six in order to have been in the KGB. But the geo-political history of the Marvel Cinematic Universe is not necessarily exactly the same as in the real world. For instance the flying car being invented during WWII means that history is not exactly as we know it. Even HYDRA (an off shoot of the Nazi party) continues for decades after WWII.
The newspaper clip that Zola shows Cap and Widow of Howard's death shows the younger Howard Stark from Captain America but should have shown the older Howard Stark from Iron Man 2. However, it is not uncommon for a younger picture of someone to appear in newspaper articles about their death. Even obituaries sometimes do this.
Early in the film Captain America pins a guard reaching for an alarm using a throwing knife through his hand. He then knocks the guard unconscious with the guard dropping to the ground even though his hand was never unpinned. The knife doesn't actually pin the guard's hand to the wall. It can be seen moving slightly even after the knife stabs it, indicating the knife merely caused the back of his hand to hit the wall.
During numerous fight scenes, Captain America falls back due to blocking hits with his shield: which absorbs nearly all kinetic energy. See other Marvel movies where he can take a hit from Thor's hammer, blasts from Iron Man, shots from aliens & ships, yet a human punch/kick causes him to stumble back.
After Fury is shot and Agent 13 gets on the walkie talkie, she says "Foxtrot is down and unresponsive. Need EMS." the voice on the other end asks if there is a 20 on the shooter. No one ever said he was shot, just that he was down.
In the street fight scene after Captain America runs out of the bus, Falcon can be seen on the overpass shooting a rifle right handed. After he yells "Go, I got this." he is briefly shown shooting left handed even though there was not time or reason to switch.
When the massive underground Insight Helicarrier launch pads emerged from under the Potomac, they should have caused waves to spread out from them in every direction, but aside from a little splashing, the water all around the pads remained calm.
During the rescue mission aboard the Lemurian Star, the Captain throws a knife through the hand of a terrorist, preventing him from triggering the alarm by nailing his hand to the wall. As the Captain is about to knock him out he pulls his hand, along with the knife, towards him, without leaving any mark on the wall.
The knife should protrude almost two inches through the character's palm, given the length of the blade and the depth of penetration.
It is said that the helicarriers will go to an altitude of 3,000 feet, which is only slightly over 900m. In reality this is not very high and certainly not high enough to fire at New York from Washington DC. The monitors merely show the targets being acquired wherever they are. It was mentioned earlier that they would fly around the country taking out their targets.
Zola was on the team that created The Winter Soldier even though he was captured almost immediately after Bucky fell to his death. But Zola explains that HYDRA rooted themselves throughout S.H.I.E.L.D. and the U.S. government, and that he himself had a key role in this conspiracy. This means when he was captured he quickly was released and went back to working for HYDRA in a secret capacity.
When Nick Fury is seen in the operating room following his shooting, both of his eyes look normal, including his left, very damaged eye which was seen when he removed his eye patch for the retinal identification.
During the climactic final fight with the Winter Soldier, Captain America is shot and stabbed, with bloody wounds noticeable. When he falls in the Potomac River following the battle, no blood is seen coming off of his body into the water.