Donatello suddenly appears in the driver's seat of the Turtle Blimp and talks like he's flying it, when in fact Leonardo was flying the whole time.
When April is calling the turtles, the turtle com is floating under a pipe. When Leonardo answers it, the pipe is gone.
After the turtles get the blimp away from Rocksteady and Bebop when they're floating in the air, there's one shot where Bebop is wearing the anti-gravity boots. He's also wearing them when he and Rocksteady are falling out of the sky after the gravity device was destroyed.
April's turtle com flips open. When her turtle com falls out of her pocket after the gravity returns to normal, it changes to the type that slides open, which is the same type the turtles each use.
When Bebop and Rocksteady enter the drill vehicle for the first time, it cannot be seen in the pipe it travels through even though the pipe is clearly transparent.
When Rocksteady and Beebop are approaching the turtle van while it's upside down, there's a shot when Rocksteady says "It's turtle trashing time". His mouth doesn't move when he speaks.