At the nuclear plant, April's eyebrows are ginger in one shot and after she falls on the ground thanking Donatello, her eyebrows are black.
When Rocksteady attacks the aliens as they start to introduce themselves, the distance between him and the aliens change as he's running towards them from where he was with Donatello.
When the aliens apologize to Donatello for him and Rocksteady getting beamed by their son, Rocksteady is nowhere to be seen after being tied to the floor.
When Shredder and Rocksteady arrive at the plant in the forcefield, Shredder is holding one of the alien's guns. In the next shot, the gun is gone. Then he has the gun in his hands again just before he attempts to attack Splinter and Donatello with the alien's gun before it disappears along with the other weapons they stole from the aliens. And then Bebop has the same gun in his hands when he starts shooting at the turtles.
At the end of Krang's intermission with Shredder on his communicator he disappears before his screen shuts off.
Donatello and Splinter find Barada and Nikto asleep, but it is never explained whatever happened to Klaatu.