Audio problem: Right after Bert kills the second graboid he gets on the radio and says "we killed that mother-humper". Val replies "...be advised there are two more mother-humpers". However Val's lips don't seem to be saying "humper". This occurs even in unedited versions of the film. (01:01:40)
Audio problem: In the opening scene when the band Black Plague is performing, the audio is out of sync and the drums aren't playing what they should be. When playing the cowbell the drummer is hitting the hi-hat, and so on. Also when hitting the snare it's out of sync, Bobby Black is also missing some notes. And when the backing vocals are heard no-one is singing. (00:01:45)
Audio problem: At the end of the movie, Carl is chasing Molly and Oda Mae. He says something like "Molly she's a thief!" and something else, but his lips don't move.
Audio problem: At the climax of the film when the Turtles are about to face Shredder for the first time, Raphael says, "I got him" and then runs to fight. When Raphael falls to the ground, his pair of Sai hit the ground but make no noise. There should be a metallic sound against the rooftop. (01:19:00)
Audio problem: When Henry asks Karen who assaulted her, she says "this guy who lives across the street from me that I've known all my life", but when she turns to face toward the camera her lips moving don't match what she's saying.
Audio problem: When Kevin is going through Buzz's private things he finds a picture of his girlfriend. Sickened by her appearance, he smashes the picture. But the smashing sound starts before he hits it. (00:22:05)
Audio problem: Just after Arnie accepts the cab driver's offer and the other one complains, Arnie's driver gives him the finger and says something like, "Eat this", but his lips don't match what he's saying. (00:52:45)
Audio problem: Near the middle of the movie, in the scene when Van Damme's friend Joshua is taking Helene money, you see that the military police have set up a surveillance across the street. They show the policeman's point of view as he is looking through binoculars. You can hear Joshua spray breath freshener into his mouth. The window is closed and they are too far away to hear this on a busy street.