Revealing mistakes: As Leonardo leaves April's apartment, we see his sword bend against the wall, indicating that it is possibly made of rubber.
Revealing mistakes: When Donatello is skateboarding in the sewers to meet with Michelangelo while Mikey is waiting for the pizza, you can see, for a couple of frames, a human hand (which should be Donny's) move in and then out of the camera viewpoint while he is doing a spin.
Continuity: While in the ground floor of the junk shop during the battle with the Foot Clan, Leonardo is seen helping April uncover an escape route. Then Leonardo is seen fending off the Foot in the background. The following shot shows Leonardo back in the same place at April's side.
Continuity: While fleeing the Foot Clan in the junk shop, the same brief scene of Donatello turning and punching out one of the Foot is used twice.
Revealing mistakes: When Raphael wakes up in the bathtub, there is a moment when Donatello laughs at a joke. As he does so he tilts his head back and opens his mouth, revealing the face of the actor underneath the costume.
Crew or equipment visible: Shortly after Casey is seen chopping vegetables with a sword, there is a shot of all of the turtles gathered in one room. In the bottom center of the screen, you can see a mic cord coming out of the bottom of a turtle's shell and going down his left leg. This is Leonardo. Behind him, another more visible cord can be seen coming out of the left side of Raphael's shell.
Audio/visual unsynchronized: During the final fight, a foot soldier is thrown into the staircase of a fire escape. He grabs his head in pain and we hear the clanging sound, but we see that his head never even got within a foot of the metal.
Revealing mistakes: Several times throughout the movie, the turtles' weapon belts squeeze their breast/stomach-plates in, suggesting they might be made of a soft material, like foam.
Crew or equipment visible: when Raph and Leo are arguing in April's apartment, there is a crew member with an orange baseball hat on trying to hide under the table
Crew or equipment visible: At the end of the movie, when Shredder is running towards Splinter with the staff, part of the sound stage is visible (on the full screen version).
Crew or equipment visible: When Splinter throws Shredder over the edge of the building near the movie's end, his puppeteer is visible (full screen only)
Continuity: During April's mugging, and the Turtles' intervention, you can see glass breaking when Raphael's sai is thrown at the light, but the light doesn't go out for another second or two.
Revealing mistakes: Right after Raphael is dropped through the skylights, he comes crashing to the ground. His brothers run to his side. As they do this you can see Donatello touch Raphael's shell. When he does this you can see the shell move inward as if it is something soft like foam.
Revealing mistakes: In the beginning, when we see Danny opening a box with a box cutter at the Warehouse, he throws it on the table and it makes an incredible bounce, proving that it's obviously rubber. Real box cutters don't bounce like a basketball
Continuity: When Rafael gets attacked by the Foot soldiers on April's roof, one of them tosses both of his sai over the edge of the building. Yet later in the movie, he has the weapons back even though he never had a chance to find and recover them.
Audio/visual unsynchronized: Several times throughout the film, Donatello uses Raphael's voice instead of using his own, like when he is punched or kicked by a Foot Clan member.
Revealing mistakes: In the scene where Raphael is fighting the foot on top of April's apartment, you can clearly see in some frames the stage that he is fighting on.
Revealing mistakes: When the Foot clan bring out the axes to fight with in April's apartment, the floor already looks like it's been hacked into before the first ax touches the ground.
Continuity: In the scene where Danny exits the sewer via the manhole cover, he slides it up and to the left. When the scene cuts to Casey Jones and then Casey Jones walking passed the manhole cover, it is noticeably down and to the left.
Audio/visual unsynchronized: The exact same sound effect (a metallic "rub") is used both when Shredder turns towards Danny after his speech, and when he lifts his spike to Splinter's neck to threaten him- yet they are two completely different actions, and the first instance doesn't even warrant the sound effect in the first place.