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: 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: When Michael and Shorty are having lunch after Michael is released, he empties the contents of the envelope onto the table. A bit later he puts everything back into the envelope, but the bullet remains on the table under a napkin. Later in the movie, Michael empties the envelope and the bullet is in it.
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: 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: 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)