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)
Visible crew/equipment: During the scene where Neo is talking to Agent Smith in the park area where Neo was talking to the Oracle, there is a close-up on Agent Smith's face. In his sunglasses you can see a bright white screen to reflect the light onto the faces of the actors. This isn't visible in any non-reflected angles. You can also see the cameraman on the other side. (00:51:15)
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.
Revealing mistake: Mr Hyde makes no bubbles when growling underwater. (01:11:30)
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.
Other mistake: Towards the end of the movie, Carmen hands a guy some 3D glasses with a crack in one of the lenses and says something like "Sorry it's the last one," but less than a minute later hands a different guy a pair of 3D glasses.
Visible crew/equipment: As the Oracle stands up from the bench, right at the end (after she says "Someday"), you can see a strip of yellow tape on the back of the bench marking the right place for her to sit. (01:54:40)
Factual error: When Shorty is removing Jennings' memories in the beginning, the pictures shown are from a third person viewpoint. If they are his memories, shouldn't these be from Jennings' viewpoint? (00:06:40)
Factual error: Both the English and French armies are wearing uniforms (English red and the French blue). An army would not have had a uniform at this time - each knight would have his own standard and colours - these colours would also have been worn by his squires. The peasants (bowmen) would wear their own clothes - usually a brown or other earth tone, and definitely not a red/blue tabard.
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.
Visible crew/equipment: When R enters the control room where Cyper is waiting and the camera moves towards Cyon, you can see the reflection of the camera in the curved glass. (01:35:20)
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)
Visible crew/equipment: When My-ek and Du-ug are bowing to the cow before attempting to behead it, you can see a crewmember's hand in the bottom left corner of the screen, holding some sort of strap around the cow's legs (probably to keep it standing still).
Revealing mistake: Near the end of the DVD version, one of the main characters (I think Deke) is chainsawing the spiders. In two of the shots, you can see the man's legs through the spider.
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.
Other mistake: Marvin survives the explosion by hiding in the refrigerator, though despite the massive blast, there is no singeing, burn marks, or even smoke around the holes that were torn into the front of the door before the explosion.
Other mistake: Garcia, in a manic moment, dips his right fingers into the bug's acidic saliva, then stripes his left cheek, where the acid eats into the flesh. A couple of minutes later, he dips the same two fingers back into the substance, and proceeds to stripe his right cheek, where the acid immediately starts eating through his skin. Oddly enough, the fingers aren't affected at all, despite being dipped into the goo twice.