Character mistake: When the revolutionary fighter commandeers Air Force One (we only know this once she's in control), a Secret Service agent is trying to break down the cockpit door by banging it with the butt of his automatic rifle. The way he's hitting the door, he couldn't break through a cereal box - it's much too weak. Presumably, the actor is taking it easy on the door because it's a cheap prop door. (00:11:15)
Revealing mistake: In one shot, it shows Air Force One on a direct heading to crash into New York, and a wall guard watches it fly by him. The movement of the guard's head does not match up with the movement of the jet as he watches it approach the city. (00:12:15)
Factual error: When Air Force One crashes into the office building, the security force monitors show the escape pod falling to the ground - inside the building. Normal physics would dictate that the pod would 'slide' across the floor of the building it crashed into, not smash through 20 floors towards the ground. We can assume the buildings are in disrepair, but it has only been 11 years since the island was turned into a prison. (00:12:30)
Revealing mistake: When Hauk finds the president's escape pod, there is a fire burning on the right of the screen. The camera was poorly placed in this part as the fire is horribly reflecting in the lenses, causing a bad distortion on screen that is highly distracting and covers the pod. (00:15:05)
Other mistake: When Snake is injected, and his timer is set to 23:00, Hauk tells him the glider is waiting. The next scene has Snake getting into the glider, but when he radios in, Hauk says there's 21 hours left. Snake was pretty upset that he didn't get a full 24 hours; knowing his life is on the line, why would he take 2 full hours to walk out the door and over to the glider that was waiting for him? (00:24:00 - 00:24:55)
Continuity mistake: When Snake finally stops the glider on the roof of the WTC, the nose of the glider sticks over the edge several feet but when the shot briefly switches to an aerial view, the nose is entirely on the roof. (00:27:35)
Continuity mistake: In the Chock Full O'Nuts diner, Snake passes a pack of cigarettes to a woman hiding in the diner. The woman lights a match and Snake tells her to keep her hand over it. The woman then says a line and lights the cigarette. At this moment, she is holding the cigarettes pack with two fingers around the top area of the packet. In the next shot, she is suddenly holding the bottom area of the pack. (00:41:00)
Revealing mistake: When Snake is escaping from the crazies just outside of Chock Full O' Nuts Diner, Snake breaks into an apartment and shoots the wall. When he breaks through it, the wall is Styrofoam. The little platelet hangs for a second or two. (00:43:30)
Continuity mistake: When Snake, Brain and Maggie drive down Broadway, away from Brain's place where the Duke is, a number of people are attacking the car as it drives. Without anyone running down the street with the car, we see a group of people twice, possibly more. Easiest to notice are 3 specific guys in the same position beside each other at both locations. (00:56:15)
Continuity mistake: When trying to escape the gang on Broadway, Snake and the others are in a yellow station wagon they stole from the Duke's men. They turn the car around to back it through a barricade of cars to escape. One shot shows their car's head lights are on, but just before it hits the barricade, the headlights are suddenly off and then are back on again in the next shot. (00:56:55)
Continuity mistake: When they steal the yellow station wagon, they are going easily 20 miles an hour. In the next shot, when escaping from the guys on Broadway, they are going at least 55 miles an hour. (00:57:00)
Continuity mistake: When Snake enters the Duke's railcar to find the President, he throws a knife at a guard's forehead. As the camera comes to the knife hitting him, we see a blood trail already on his face from that wound, before he could start bleeding. (00:59:30)
Continuity mistake: When Snake first rescues the President from the Duke's railcar, the two of them walk beside the train. They walk the whole length of car #2205, then they walk it again. The 'new' car has some graffiti on it; either the filmmakers used both sides of the car, or added the graffiti to make it look different, but they forgot to change/erase the car's big yellow numbers. (01:00:10)
Continuity mistake: When Snake kills the wrestler he falls forward shoulders forward, next minute his arms are over the ropes, next minute his arms are in a different position again - quite active for a dead man. (01:16:55 - 01:18:10)
Continuity mistake: When Snake kills the wrestler, he does so by jamming the nails of his spiked bat into the back of his skull. Snake releases the bat, which stays stuck to the wrestler's head. The next shot, the bat is now missing as the wrestler falls forward against the net, dropping his own bat to the floor. But Snake's bat is nowhere to be seen. Then a few moments later after Snake activates the tracer, the bat is shown on the back of the wrestler's head as he is slumped over the net, which Snake knocks off. Yet the wrestler's own bat is no longer seen, which was by his feet before. (01:16:55)
Factual error: The wrestler is killed by Snake stabbing the back of his head with a spiked bat, having rather long and thick spikes on it. As the Wrestler falls against the net, the back of his head is shown as he is slumped over the net. There is no wound on his head, nor any trace of blood, despite having one or more large spikes just jammed into it. (01:16:55)
Continuity mistake: On top of the World Trade Center, some "Redskins" are rocking the Gulf Fire back and forth over the edge and cut it loose. You see very large red markings on the Gulf Fire's wings. But when you see it falling in the next shot towards the camera, the red markings are gone and the wings are solid black. (01:19:30)
Continuity mistake: As Snake makes it back up to the top of the World Trade Center, he sees Brain, Maggie, and the president in a fight with a gang of "Redskins". The Redskins cut the line on the Gulf Fire and it plummets to the ground. Maggie, Brain, and the President are hiding behind some air ducts and tubes. just before the shot cuts, the President pops his head up and looks around, making his head the highest of the 3. Maggie is holding her gun pointing up, and Brain is sitting still just looking at the President. It then cuts to an angle behind them. Suddenly the President is down on his hands and knees again, Maggie is holding her gun lower and sitting up straight, and Brain is leaning back looking like he is about to fall over. (01:19:35)
Visible crew/equipment: When Snake is back on top of the skyscraper to get to his glider you can see the elevator doors sliding shut behind him....and the fingers of the people pushing them. (01:19:50)
Plot hole: When Snake, Brain, Maggie, and the President get to the car at the WTC, Snake opens the hood when the car is dead, and somehow he is out in the open when the Duke is about to shoot. First, how would he get there with a crossbow trained on him, and second, how did Maggie pass the revolver to him, when he hands it to her to open the hood of the car? (01:21:05 - 01:21:50)
Suggested correction: When the hood is opened Maggie can be seen immediately putting the revolver behind her back. Being stood very close to Snake it's assumed it was passed to him offscreen. With the crossbow trained on Snake the Duke monologues directly to Snake allowing him to step a foot or so away from the car to look like he's listening and going to accept his capture but ultimately it was to have a shot at the steam engine and create a distraction. Maggie took out the crossbow guy by slamming the hood on him.