Continuity mistake: In the end, when the President is visited by the X-Men, he receives a blue binder, which is laid in front of him on the table. When they have left, you see a shot including the President's desk, and you can see that the only thing he has on the table are some sheets of paper, stapled in the upper left corner, opened up. Then the shot changes to a close-up of the President, and then back again, and you see the blue binder in front of him, closed, and the papers have disappeared. (02:01:40)
Continuity mistake: When John and Catherine are in the hangar at the runway, the Cessna's tail number is N3035C. When the plane is shown in the air, the number is N3973F. When they land, the tail number has changed back to N3035C. (01:22:25 - 01:25:50)
Continuity mistake: During the freeway scenes, the katana Morpheus used as a foot hold to grab the keymaker keeps moving. It was at arm's length from the top when he inserted it; when Morpheus was standing on it, the sword was a whole body length below the top; when Morpheus took the sword out in his fight against the agent, it was back in its original position.
Continuity mistake: On the ship, Dr. Zimsky reveals that project DESTINI is an acronym and that the last letter is "I" and not "Y." (INI standing for INItiative). When Rat is at his computer, he goes to the website for Project Destiny, with a "Y" and not an "I." This same thing happens when the Project Destiny subtitle flashes across the screen.
Continuity mistake: Near the beginning, when Banner arrives at the lab with his helmet on, he removes the helmet when he sees Betty. A close-up of his face is shown and his hair is messy with part of his fringe on his forehead. Betty is shown quickly, then the same shot of Banner is shown again, but this time his hair is perfect.
Continuity mistake: When the members of the League are attacked at Dorian's home, the fight is accompanied throughout by a blizzard of paper falling from a height, yet hardly any of the books have been disturbed on their shelves. (00:28:40)
Continuity mistake: Sati and her family leave one suitcase when they get on the train (the one Neo was carrying), but when the train comes back and Trinity steps out, there is no suitcase. It can't have gone anywhere - as we see when Neo tries, the only way out is on the train, otherwise you're caught in a loop. (00:14:05 - 00:24:00)
Continuity mistake: In the scene where the police car is chasing Ben Affleck and Uma Thurman on a bike down in a tunnel, in one shot, the police car's flashing light on top is ripped off by the low ceiling. In the very next shot, the lights are still on the top. The next shot shows the lights are gone. (01:13:50)
Continuity mistake: In the scene where Juni finds Carmen in Level 4, they are on a cliff. They begin crossing a virtual bridge, then in the next shot, they are back on the cliff.
Continuity mistake: The cracks on Henry's diploma after the missed shot change between closeups and totals.
Continuity mistake: Nino gets trussed up in silver duct tape. The boy gets bundled over the shoulders of one of the bad guys, and you can see that there is only a small amount of tape around his legs. They go straight inside the meat packing factory and suddenly in the next shot, there is a huge amount of tape around the boy's legs.
Continuity mistake: Marion isn't wearing any clothes as they enter the convenience store. However, as they are standing in the doorway you can see he is wearing boxers.
Continuity mistake: When the team climbs out of the river they suddenly are very dry. Best evidence for this is their hair and clothes when they start to run away (those should have been heavier). (00:27:45)
Continuity mistake: As John first checks in at the Baker motel, the pen on the desk shifts between shots. It's on a chain and certainly would make some noise if either character had moved it. (00:10:45)
Continuity mistake: When Earl de Darkwood is holding a phone on the plane, his earring appears in his left ear. Later when he is shown exiting the limousine, the earring is now placed in his right ear. (00:19:30)
Continuity mistake: When Kurt and Markie are racing together in the Ice Leg, if you look closely at the part when Markie is about to crash into chunks of ice, Kurt's car has no graphics, and a lighter green windscreen.