Continuity mistake: 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. (01:09:05)
Continuity mistake: When 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 appeared. When the shot changes back, his wrists are bare again. (00:56:50)
Continuity mistake: 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. (00:34:00)
Audio problem: When Leonardo stops Daimyo, the words "Hold it, Bucko" are heard, but Leonardo is not seen to be speaking at all. (01:15:30)
Continuity mistake: Whit and April are fighting by the spring, and just before it cuts to Mitsu preparing an arrow, Elias Koteas is pounced by a guy wearing colorful rags in black, orange and yellow patchwork, a blue and white pattern bandana and black and white striped legwarmers. Behind Mitsu, meanwhile...a guy with the same horrid fashion taste is charging. What are the odds. (00:39:35)
Other mistake: After Leonardo revives Yoshi, he picks him up, hugs him and touches heads with each other as they hug but Yoshi pretty much moved his head immediately and Leonardo continued sitting there as if their heads were still touching. It looks like the actor didn't realise the child moved away and they never reshot it. (00:48:15)
Continuity mistake: When Michelangelo's horse is about to stop galloping, the wide shot shows his right hand lowered and his body bent downwards, but in the close-up his hand is raised. This swaps back and forth. Seemingly, the wide shots were of a puppet of some sort used for security reasons.