Continuity: In the scene where Raphael meets Yoshi and talks to him about being a kid and having fun; if you look at Raph's wrists you'll notice that he is not wearing any wrist bands as he usually does as with the rest of the turtles. However, when Raph puts his hand on Yoshi's shoulder there is a close-up of Yoshi's head and shoulders. Look at Raph's wrist in the close-up and you'll see that a wrist band has magically appeared. When the shot changes back, his wrists are naked again.

Continuity: When the Turtles are climbing the wall to get into the garbage-chute that leads to the prison, you can see Donatello's bandana tail hanging down towards the wall just as if they were crawling on the floor.

Continuity: When the turtles go sliding down the ramp down into the sewer, watch the inside of the ramp before Raph comes out and you can tell where they stooped recording and restarted it. The shadows seem to change places. This also happens right before Leo comes out too.

Continuity: When the turtles travel through time they switch clothes with the other people they are switching with. But, if they are totally switching clothes. Why do they still have head bands on?

Audio problem: When the Leonardo stops Daimyo, the words "Hold it, Bucko." are heard, but Leonardo is not seen to be speaking at all.

Audio problem: When Walker confronts the Turtles in the Daimyo's courtyard, he says "My God, who's your tailor?" One of the Turtles says "We're naked." but none of the Turtles' mouths move.

Revealing: At the end of the movie when the villain falls into the water, you will see that the splash appears before he hits the water.

Continuity: When the time traveling first beings, it is explained that the dynamo and the high ranking people in the palace speak English because of the trade and western influence of their partnerships with the westerners in the movie. But later in the movie, all the common towns folk speak english with the turtles and rarely use japanese.

Revealing: When the turtles are holding the scepter and it starts lighting up, you'll notice that Michaelangelo isn't even touching the cepter; he's just holding his hand up, so he shouldn't have been sent through time.