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.
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: 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)
Revealing mistake: In the opening of the movie, a citizen is reading his copy of the New York Post and you can actually read the date; Wednesday September 12, 1990. It is obviously a movie prop though, because the scene was shot in late 1989. How can you tell? Easy; he is reading it next to a newsstand kiosk full of magazines from that period; instantly recognizable are Vanity Fair's November 1989 issue with Baryshnikov on the cover, and GQ from December 1989 with Sting sporting an epic 'stache. (00:00:50)
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. (01:23:00)
Revealing mistake: In the middle of the fight inside April's apartment, there's a comedy/action bit with Leonardo repeatedly trying to slash at Foot Clan guy. Ultimately he fools him and kicks him. Behind him another two bad guys arrive, but there's a very awkward bit in the choreography where one of the guys quite literally does not know where to go and puts himself in a corner with nobody there stumbling into the other. (00:43:30)