Other mistake: In the music within the ending credits, the lyrics incorrectly state that Raph is the leader of the group when all Turtle fans past and present know it is Leo.
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)
Revealing mistake: A lot of times in the movie, when the turtles' mouths are wide open, you can see the cast. An example of this is the scene when Raphael wakes up in the bath tub and Leo hugs him. When Donatello tilts his head back and laughs you can see eyes, a nose, and a mouth within the mouth of the costume.
Revealing mistake: In the scene close to the end when the turtles are fighting the foot soldiers on the fire escape (directly before the scene where Mikey ducks under the foot soldier's axe), Raphael thumps a foot soldier on top of his head and then rams the soldier's head into the stairwell. The only problem is the soldier's head misses the stair by about a mile. The sound effect of impact is there and the soldier even holds his head as if he were hurt. (01:17:20)
Revealing mistake: In the scene where Raphael is thrown through April's skylight after being attacked by a few dozen members of the Foot, the other Turtles and April check on him. As Donatello and Leonardo look him over, they lean on his shell, bending it with great ease even though a turtle's shell is supposed to be almost as hard as rock.
Visible crew/equipment: After Casey takes a golf club and drives Master Tatsu into a pile of boxes, a camera lens hood is visible on the left side of the screen. It can be seen again in a later shot right before Casey and Danny carry Splinter away (full screen version). (01:14:40 - 01:15:50)
Other mistake: After Michaelangelo hums to agree with Donatello's comment moments after Casey & April have finished arguing and slamming doors, you can hear Michaelangelo humming "Old MacDonald," but you can see a shoulder strap and a purple headband indicating this is Donatello. (00:52:15)
Revealing mistake: When Raphael is fighting the Foot Clan on the roof of April's building, after he tells them that they must be studying the abridged book of ninja fighting, he kicks one of them in the stomach and then cartwheels over his back to kick another one in the face. You can tell he misses the second one by a mile, but the man still groans and collapses unconscious into the chair behind him. (00:40:45)