When the Decepticons land in an alligator-infested lake, they appear to be human sized, compared to the reptiles. In reality, the alligators would be dwarfed by them. It is also interesting how the alligators attack these gigantic robots. One would think they'd be frightened away.
In one interesting shot, when the Decepticons are shown flying and Starscream is the closest to the screen, they forgot to animate his face. You can see his helmet and his eyes, but no head was drawn under them. He even continues to talk this way.
In the sewer-scene, there is one shot where no water was animated, and all the characters seem to be floating in the air, with only their upper body-parts being visible. You can see waves in the air, but no water.
As Aron gathers some Energon-cubes from his chest of drawers, his body slowly disappears - at the end of the shot, he has no head and other body-parts are missing as well. The animators must have gotten the animation cels mixed up.
When the giant aliens are trying to cut open the Decepticons, their huge buzz-saw's blade doesn't seem to move, yet you can hear the sound it makes. It is even shown to shake, but the blade simply doesn't spin.
The shot in which the Autobots board their rocket is perhaps the most error-filled shot of the whole cartoon. All of the animation cells are messed up, so the Autobots actually go in front of the rocket (rather than into it), and Nitro the alien cat can also be seen covering the rocket, when he is supposed to be behind it. Then, as Aron closes the door of the rocket, his hand also passes behind Nitro. Notice how the lower body of the Autobots and Nitro are not drawn in, making them look like huge blocks of colors.