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.
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.
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.
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Revealing mistake: After Splinter releases the nunchaku from Shredder's spear, he falls from the building's ledge. But notice how Shredder stops abruptly right before the series of shots which show him taking the long fall into a trash compactor, indicating that he actually lands on a mat.