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)
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: 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)
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)
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)
Audio problem: Battling the Norinaga soldiers in the castle, Donatello parries several katana strokes using his wooden bo, which causes sharp metallic sounds every time. (00:22:50)
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)
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: Walker witnesses the music playing and the guards wrecking the demonic machine; he constantly has his left hand held up in the air in the close-ups, but in the other angle he shifted that hand to lean against the door. (00:15:45)
Audio problem: April's walkman keeps playing for a while spreading in the air the suave notes of The Barrio Boyzz's "Conga" even when the batteries already came out on the first strike. (00:15:40)
Continuity mistake: April's walkman is very conveniently prone to play randomly. She puts it down on the floor, but it is, together with the headphones, positioned differently practically at every shot in particular when the guards start bashing it and everything is closer together in close-up than in wider angles. (00:15:30)
Continuity mistake: In the sequence set in present time when the Turtles interact with Kenshin, once he faints seeing the giant Japanese-speaking rat the shopping bags on the table changed position - the blue bag the wind knocked on the floor is back, and the red bag is up and not horizontal. (00:12:00)
Continuity mistake: Leonardo shouts "He's a man!" when Kenshin appears in the Turtles' hideout; he is holding in the foreground with the right hand his book about katanas, but in the next shot it's on the table, under his left hand. (00:11:35)
Continuity mistake: April materializes in the same spot as Kenshin; her headset is placed away from the collar of the kimono. She is still in the same position when she spots the priest, but the collar is underneath the headphones now. (00:11:50)
Continuity mistake: Kenshin throws a temper tantrum in a room with several statues. The doors open and a strong wind blows; the position of the scrolls on the table changes between shots; they are first closed by the edge of the table, then unfurl from a position much further behind. (00:10:10)
Continuity mistake: Walker's henchmen dump on the court Lord Norinaga's sentinels and walk away. They are already shown posing with evil smirks and all that in the next shot while Walker is doing his threatening speech. (00:08:55)
Continuity mistake: We first see Lord Norinaga in a close-up looking at his son's arrival. His helmet is tied under his chin, but when he walks in the helmet's cord is split above and below the chin. (00:07:40)
Other mistake: When April O'Neil arrives bringing gifts, she leaves the manhole cover completely open - there's also an awful lot of light coming from there, as if the abandoned subway station were built inches away from the surface. (00:05:20)
Continuity mistake: During the introduction of the turtles, Michaelangelo's bandana goes from the back of the shoulder to the front and then both ends behind the shoulders between shots. (00:04:30)
Continuity mistake: Kenshin loses his sword battling with the guards at the beginning of the movie. The sword gets stuck almost horizontally in a tree stump. Then one of the guards grabs it as he rides by with his horse, but the katana is now stuck in the tree at a sharper angle which makes it possible to reach for it and grab it on the fly. (00:02:35)
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