Plot hole: Michelangelo ends up in the forest completely by chance because he can't ride and his steed dragged him away from battle. Not only Mitsu is there in wait exactly on the tree branch he'll pass by, but also a bunch of villagers are standing by with a cart to fetch him. There's no possible reason why the leader of the rebellion would be lurking in wait setting up a trap in that random spot in the woods, away from battle, where no Norinaga soldier would be. (00:25:30)
Continuity mistake: When Michelangelo shouts "Woah! Good horsey! Good horsey!" the scepter goes from his left hand to his right between shots. (00:25:35)
Continuity mistake: When Michelangelo loses consciousness and his helmet, the helmet rolls on the ground above his head, but when the rebels are approaching to pick him up and haul him on the cart the helmet is by his shoulder. (00:26:10)
Other mistake: Not finding his scepter anymore, Norinaga speaks in English to the guards. It's rather stupid of him to do so since it's counterproductive to show vulnerability to his 'ally' he wanted dead at the beginning, but let's forget that. The problem is that his envoy addresses the Turtles outside the gate in English as well. He thinks they are the honor guards, fellow countrymen, there's no reason why he'd use English. (00:28:00)
Continuity mistake: When the guard tells Norinaga about his honor guards; "They're coming! They're behind the wagon!", Norinaga's hand placement changes between shot and reverse. (00:28:15)
Other mistake: Apparently, Whit is the only prisoner in Lord Norinaga's dungeon who wants to be set free; everyone else does not react to the fight, ask to be released or struggle in any way. (00:33:00)
Audio problem: April is lowering the cage where a random doppelganger of Elias Koteas appeared in Feudal Japan. She says "I know I am gonna regret this", but her lips are not moving. A moment later she shouts "Well, come on!" and again there's no articulation of sounds from her mouth. (00:33:00)
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: Raph quotes Terminator just before he jumps in the waste disposal chute, but the animatronic's lips don't move. (00:34:00)
Continuity mistake: The Turtles are fighting the rebels by the springs. The first time we see Leonardo fight some of them off, his first action is hitting (with the side of the sword, we assume, or he'd slice it) the head of a guy, but the 'hit' is really a miss, since no contact is even remotely made. (00:38:20)
Continuity mistake: April screams and squirms to free herself from the arrow that pins her sleeve to the tree. Her hand is in a different position in each shot. (00:38:30)
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)
Revealing mistake: When Raphael tosses the sai breaking Mitsu's arrow in two as she is aiming at April and Whit, before it cuts to the close-up the actress is smiling as she turns around, obviously pleased because the take of the throw worked. (00:39:45)
Revealing mistake: In a complete non-sequitur, the Turtles declare that they are friends, taking off their masks. Mitsu picks Raphael's helmet up herself; not only her hands chance place on the helmet at the cut, but the helmet is soft rubber under her fingers. (00:40:25)
Continuity mistake: In Niles' POV, during their first confrontation in the middle of the village raid Walker on his horse is in the shade, facing Michelangelo in sunlight. It's the opposite in their respective close-ups. (00:44:15)
Audio problem: Michelangelo runs inside the burning hut yelling "Here I go!" with his mouth closed. (00:46:10)
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: Leonardo picks Yoshi up from the ground after reviving him; his bandana goes down his left shoulder, but in close-up goes down both sides of his neck. (00:48:30)
Factual error: Raphael tells Yoshi that being a kid, he shouldn't think about war but rather fly "one of those things." He is pointing at kites who have artwork (kabuki-ish makeup with the modern japanese flag) that looks out of place for 1603. (00:56:40)
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)
Answer: It might just be incidental music, but it sounds more like a variation of "Yoshi's theme" (an original score for the film), which was meant to sound like traditional Japanese music.
Bishop73