When April and Irma win the pizza, the pizza is about a normal size, but at Irma's apartment, the pizza is smaller when she heats it up.
When Raphael says, "Quick, Donatello, some tomato sauce!" while he's spinning the pizzas with his Sais, he's seen with Donatello's colors.
When Michelangelo removes a slice of pizza from the box to give to April instead of the pizza itself, he moves the pizza box in his hand a little. When he does, a slice of pizza appears out of nowhere in the spot where he originally picked up the slice. Then the blank spot from the slice he picked up reappears when he slightly moves the box back to the original position he had it and puts the slice back.
When Leonardo helps Shredder get out of the way from being attacked by the pizza monster, the next scene Shredder scorns Raphael and he responds in Leonardo's voice.
When Raphael says "I can practically smell him" his mouth doesn't move.