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)
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)
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.
Other mistake: After Leo's failed attempt of fighting Shredder for the first time, Mikey and Donnie then play Rock, Paper, Scissors to see who fights Shredder next. It then cuts to Casey talking to "The Foot" where you can hear Mikey fighting Shredder. The next scene shows all four Turtles in a huddle regrouping, breathing heavy, and out of breath. According to what we heard, Donatello shouldn't be out of breath as he has not fought Shredder for the first time yet.
Continuity mistake: When Danny is admiring April's turtle sketches, he asks if he can keep one of them. His right hand holds onto a sketch of Leo at first, but in the following shot his right hand isn't gripping the sketch at all. Instead, he's seen reaching out to pick it up from the couch. (01:04:35)
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)