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.
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)
Continuity mistake: After Raphael has a fit and walks out of April's apartment, he goes up on the roof to vent his anger for a while. Pretty soon, Casey spots him from another rooftop several buildings away while tuning a radio. As Casey looks out at Raphael's faint image in the distance, pay close attention to the background as well as the white building Raphael is standing on (you can notice the Empire State Building among other landmarks). When Casey grabs some binoculars to take a better look, Raphael can be seen resting on a brick ledge. In the following shot Raphael looks out at the city towards Casey's vantage point, but from Raphael's position, the Empire State Building - as well as the white building where he was venting just moments before - are visible on the skyline. Somehow Raphael has managed to relocate to another building's rooftop between shots. (00:38:15)
Continuity mistake: When Splinter flips Shredder over the edge of the building, Shredder pulls a knife and throws it. When Splinter catches the knife, he catches it with his right hand; in the next shot, Splinter's right hand releases the nunchaku and Shredder falls. The shots are out of order.
Continuity mistake: In the alphabet game of insults, Donatello calls Casey Jones "elf lips." Casey puts the monkey wrench on the radiator next to the dirty rag, but in the next shot the tool is gone from there and is in his left hand instead, so he retrieves only the rag from under the hood. (00:53:10)
Continuity mistake: Casey Jones arrives to the save the day. Michelangelo does a Wayne Gretzky reference. Notice in the background Master Tatsu, solitary and surrounded just by old abat-jours and other dusty curio. When he orders in his spartan English to "attack", he suddenly has a bunch of goons all over him. (00:46:05)
Continuity mistake: At the beginning of the movie, the stolen wallet ends up in Danny Pennington's hand who is tasked to hold it out for the ninja to grab it. In close-up Danny's hand is positioned below the sleeve of his T-shirt, in the shots before and after his hand is higher, between the sleeve and his body. (00:01:15)
Continuity mistake: Just after the Turtles train by fighting with each other, Michelangelo is in the barn punching the punching bag. The very next shot is Raphael on top of the barn shouting out Splinter's name. Upon further inspection at the weapon at his side, this is not Raphael. It is Michelangelo. (00:56:45)
Continuity mistake: During the fight in April's apartment, The Foot Clan member swings his weapon at Donatello and misses knocking out the power as seen by sparks which causes the fire. Somehow April's answering machine still works, though.
Continuity mistake: When Raphael angrily leaves and practices his Ninja moves on the roof, he appears on a white building. When he is thrown through the roof down to the other Turtles, it is still a white building. The building in which the Turtles fight The Foot and catches fire is the "Second Time Around Antiques and More" shop where April lives which is brick, not white.