The design of Devastator's face changes from shot to shot. He has two eyes in one shot, for example, then a visor in the next.
Rumble is seen driving the subway. A moment later, he changes to Frenzy.
Optimus Prime is seen having both of his arms on Megatron's monitor screen. However this scene takes place before he managed to reattach it. When he transforms into a truck, he is again seen having his other arm.
After the Autobots have finished rebuilding Optimus Prime, half of his chest is still shown lying on the ground. Then, it disappears.
The shot that shows us the entire Decepticons' base of operations is shown twice, even when the characters we see in the shot aren't supposed to be there.
After the Decepticons' metal tower emerges, the shot freezes, and so does the cloud of dust that should still be moving.
As the Autobots enter the canal, they are animated from the front. Yet the background moves to the side, making it look like some of the Autobots are walking off into directions, rather than walking in a straight line.
When Megatron is talking to the disabled Prime, his arm overlaps one of Prime's smoke-stacks, when he is supposed to be in the background.
As Scavenger is bashing the ceiling to get Optimus Prime to fall into the Constructicon's trap, the cracks in the ceiling also appear on Scavenger's digger arm & bucket.
Megatron's gun barrel mounted behind his right shoulder is colored black in most of the story. Normally, it's colored white.
Optimus Prime says to Ironhide, "That's the way to cool it, Ironhide!" for no apparent reason, since Ironhide wasn't doing anything in that scene.
Spike commands Bumblebee to turn left. Then they all turn right.
In keeping with the traditions of the cartoon villains of the era, Megatron's plan to get rid of Optimus Prime - making a crocodilian out of his body instead of simply destroying it - makes little no no sense, and is also inconsistent with future story, where Prime is revealed to have had the Matrix of Leadership inside his chest all along. Megatron would never let such an important artifact slip out of his hands, yet he does.
The robot alligator that the Constructicons built out of Prime's body has a blue tail. The only large blue pieces on Prime's body are his legs, however it is revealed that they weren't used to construct the alligator. Also, it is shown having both of Prime's smoke-stacks. This can't be either, since one of them is still attached to Prime's arm at this point.
When the Decepticons capture Optimus Prime, a large green object is seen erupting from the ground around Prime. In the following shot, he is shown falling several hundred feet into the Decepticons' underground base. So what was that green object? It looks like Scavenger's shovel, but that cannot be possible, since Scavenger was nowhere near the ground.
After Mirage claims "This alligator is big and heavy!", Optimus Prime replies "I'd say a little of both." This does not make sense.
Megatron responds to Soundwave's report by saying "Excellent, Scrapper!". The word "Scrapper" should be heard in his next sentence, since he is (obviously) talking to Soundwave at this point.
Optimus Prime is using a rope to climb up the side of the Decepticon Tower, but at the time, he only has one arm, so there would be no way for him to pull himself up.