When Shredder gets his personality back for the first time and tries to lunge at Splinter but gets restrained by Michaelangelo on his right arm and Donatello on his left arm, two shots later its Leonardo on the right and Raphael on the left, next shot, it's Michelangelo and Donatello again but Michelangelo has Leonardo's belt buckle.
When the turtles come to rescue Michelangelo, the sock that was in his mouth is missing in one shot, then it's back in his mouth again the next time we see him.
When the Turtles head for the building where Michelangelo is being held, Michelangelo is among the Turtles heading to rescue him.
When Shredder speaks to Krang on the communicator, Krangs position changes from being in his android with his tentacles inserted though holes, to not being in the android at all, to being inside the android without his tentacles in holes, within the same short conversation.
Krang said when they replace the president with a hologram, he would take control of the most powerful office in the world. But the president only runs the United States of America, not the entire world.
When Michelangelo calls his name to Shredder when trapped in the force field, the force field is not showing when he calls it.
At the pizzeria, Shredder gets his personality back by finding leftover cheese in a shredder. Yet, when the Turtles use Michalangeo's name seconds later, Shredder doesn't revert to the Michalangelo personality.
When The turtles arrive to rescue Michelangelo, one one them shouts his name, but Shredder who is nearby does not react to hearing the name, like it's been established he should.