When Raphael is having his heart to heart with Yoshi, one of his wristbands is missing. When he joins Yoshi in flying the kite, his wristband has reappeared.
Walker never grabs the scepter after he rescues his bird, a sack just appears over his shoulder holding it.
Somehow, both Michelangelo and the Warrior with whom he switched times with return to their respective times wearing the same Hawaiian skirt.
When the turtles tell April they plan to rebuild the scepter, April has black trousers on but in every other scene her legs are bare.
Leo ducks a cannon shot and his bandana straps are over the front part of his shoulders, actually going into the inner part of his shell, next shot they are back behind his shoulders.
The women's kimonos are folded the wrong way. A kimono's right side is always folded underneath the left side.
When the ninja turtles are running across the clay tile roof you can see that the tiles bounce like rubber as they run across them
The Turtles have two massive holes below their masks, for the actors to see out of.
When Splinter tells the Turtles that the scepter will be in the temple, the footage of him talking is halted in mid-sentence and rewound as he says "You will be replaced..."
When Raph says "I'll be back" when rescuing April, his mouth never moves.
While being destroyed, April's Walkman keeps working (for a moment), even after the batteries have fallen out.
When April's walkman first starts playing after she arrives in Japan, the headphones are not plugged in, yet the music is still audible.
Yoshi's mouth moves alot during the CPR scene.
Raphael goes to see Yoshi and gives him a yo-yo. Raphael promises Yoshi that tomorrow afternoon he'll teach him some tricks on his yo-yo. But by tomorrow afternoon Raphael, his brothers & April should be long gone back home as they only have 2 1/2 days through the space time continuum to do what they need to do before going back home to the present. So Raphael made a promise that he wasn't going to be able to keep to Yoshi.
When a couple of the Daimyo's soldiers call out the Turtles, Donatello, in a moment of panic, replies "Ohayo wasabi." Ralph points out that this phrase is nonsense, and Donatello claims his Japanese is "a little rusty." However, this scene takes place in the evening. The correct term should be "Konbanwa." (Good evening.) Donatello accidentally butchered "Ohayo gozaimasu." (Good morning.) Looks like he's more rusty than he thought.