Continuity mistake: When Curly Bill is shooting up the town while drunk, he fires about 10 more rounds than his six shooter can hold without reloading (so too many shots even if he had a second gun), and still has a round remaining when he shoots Marshal Fred White. In the 1880 court hearing held after Marshal White's death, Curly Bill still had 5 rounds remaining in his pistol.
Visible crew/equipment: In the fight scene on the stairs near the end of the movie, the camera shot looks up and there is a security camera mounted up in the corner. (01:29:40)
Plot hole: The opaque red lined map that Otomo retrieves from his first fight is ridiculous. Why would people who know where the hidden base is be carrying around a map on them (which shows a route so basic that they'd have to be brain-dead not to be able to remember it anyway) just so that conveniently one of their enemies can get it?
Continuity mistake: Kimble dyes his hair very dark to escape detection and dyed hair fades over time. For the rest of the movie his hair noticeably goes from darker shades to lighter shades and back again showing that the scenes were shot non-sequentially on different days with a fair amount of time in between.
Factual error: When Jean-Claude is chased by the helicopter in the woods alongside the river, the man in the helicopter fires a MP5 machinegun, but it causes huge explosions, this is impossible, it's not a grenade launcher!
Audio problem: When Miss Orchid is making dinner for Wong Kei-Ying, she turns to him and tells him about a special chili that is made. When she turns back to her cooking, she tells him how hot it is but her mouth doesn't move.
Other mistake: In the scene at the beginning where Phil eats Jason's Heart, you'll notice that he screams like a monster for a bit. Don't you think that the two security guards would easily hear the screaming and intervene, being that they're in the very next room? (00:13:40)
Continuity mistake: In the locker room, after Dex's death, TJ punches Franz. Karl comes into the locker room and tells TJ to go home. However, a few seconds before the punch we see Karl come into the room point at Franz and say something. You can't hear it because the audio of his line was deleted.
Continuity mistake: When the Turtles are climbing the wall to get into the garbage-chute that leads to the prison, you can see Donatello's bandana tail hanging down towards the wall just as if they were crawling on the floor. (01:09:05)
Continuity mistake: When Smith and Connor arrive at the Nakamoto tower and are exiting the elevator on the 46 th floor, you can see in several shots that Smith's suit is wet on the shoulders. However as he was going up the elevator the suit wasn't wet at all and even during the whole scene in the 46th floor, the suit changes from wet to dry as angles change.