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)
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.
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.
Continuity mistake: In the scene where Raphael stops to listen while carrying a KO'd April through sewer tunnels, her position in Raph's arms reverses between shots. Furthermore, April is obviously played by a doll in this scene, since her limbs jiggle quite unnaturally when Raph moves.
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)
Continuity mistake: Near the end when the Turtles are fighting Shredder and Splinter makes his appearance, you can see Mikey starting towards Splinter only to be held back by Raph, then a few seconds later, when Leo rolls to the group, the scene happens again, Mikey heading towards Splinter with Raph pulling him back. (01:22:28)
Continuity mistake: During a fight sequence between the Foot Clan and three of the turtles in April's apartment, keep in mind that April is still tending to an injured Raphael in the living room. But as the floor collapses into an antiques store below, you'll be able to spot her on the lower left side of the screen shielding her eyes from debris - instantly in the store before anyone else (except for Master Tatsu and several other Foot members, who were waiting there to begin with). (00:44:15)