Continuity mistake: In the scene where Hot Rod and Kup are stuck underwater, we see Hot Rod fighting a Giant Squid. Just after the Giant Squid swims off we see a shot of Kup lying on the ground with his right arm and his left leg missing. However, when Hot Rod gets to him they have swapped sides, the left arm is missing and the right leg is missing (don't be confused by the fact Hot Rod flipped him). Only two of Kup's parts are missing, as we only see Hot Rod pick up two parts.
Continuity mistake: During the fight scene between Optimus Prime and Megatron at Autobot City, Megatron pleads for mercy. He reches for a gun that is under some metal. The gun is black in colour. Then Hot Rod jumps on him, Megatron stands up and the gun is now purple. It then goes to a close up of Megatron with the gun in one hand, and Hot Rod in the other, and the gun is now black again. (00:22:00)
Other mistake: When Perceptor pops up to tell Blaster to radio Prime, Blaster acknowledges that Perceptor is there before he even sees him. And I doubt he could of heard Perceptor because of the amount of noise the lasers were making, and Perceptor didn't make any noise. (00:14:45)