Revealing mistake: There's one scene where the Turtles are surrounded by the Foot. Leonardo reaches behind him for his katanas, but he doesn't unsheathe them. If you look at his elbows, you can see gaps in the pads where the actor in the suit hasn't fully fastened the gloves to the rest of the outfit. (01:05:40)
Continuity mistake: After leaving the Bookseller store, in an overhead shot Belle passes a shop just as a woman is pouring water towards the downspout, and in the next shot the shop suddenly has a large hanging pipe sign with a table under the window, the green shutters have vanished on the right window, the half-timber wall pattern and wood trim have changed, etc.
Revealing mistake: Junior can't get on the Crazy Dance because he is a milimeter too short. After seeing Murph (the 20-year old in his class) and Trixie (on heels) get on it, Junior speeds up the ride and all the kids on it get dizzy and barf everywhere. If you look where the puke shoots out, it's a bit obvious it's not coming from their mouths, but from a point behind them. Most obvious are Trixie and the boy wearing glasses.
Other mistake: When Gomez begins to flip through his desk calendar, we see that "today" is Thursday, March 28, 1991. He then turns to the date of the "next quarter". The left hand page shows Thursday, August 8, but the right hand page shows Tuesday, September 9. (00:11:15)
Continuity mistake: When Steve Martin is going berserk in the grocery store he is wearing white socks as he runs away from the assistant manager. In the next scene in the jail cell, he's wearing black socks.
Continuity mistake: When Pockets is shooting paint at the pirates, he sprays yellow paint on a pirate's face on the right, who crouches and touches his face blinded. Shot changes and not only is the painting gone, but the pirate is calmly sword fighting with a kid. (01:53:38)