As the Autobots are discussing all that has happened, Prime turns gray for a moment. By this time, his protective paint has either worn off, or he has been painted over with his true colors.
Wheelie, who was listed amongst the casualties in the confrontation with Superion, is absent when the other Autobots are retrieved and revived. Yet, Blaster, who wasn't in that fight is instead appears in his place.
When the Autobots all drive off in the last scene, Kup is drawn backwards, making it look like he's driving in reverse.
Early in the story Prime is talking to the surviving Autobots, many just revived. The bottom of one side of his head covering is colored gray, instead of blue like the closer side to the viewer.
If the substance they coat Optimus Prime with is so resistant to external effects as the characters claim, how did they melt it into a liquid in the first place?
Swofford and Morgan seem to have gotten off easily for what they did. Considering though they almost doomed the world.
Galvatron states as a fact that Autobots, as a rule, cannot fly. While this rule has become accepted since then, in earlier episodes, Autobots were shown to be capable of flight.