Continuity: In the battle scene at autobot city, Megatron orders Soundwave to jam the transmission that Blaster is sending to Optimus Prime. When Soundwave ejects Rumble, Frenzy, Ravage & Ratbat we see them flying through the air transforming simultaneously and and both Rumble & Frenzy are coloured the same (red & black) when Rumble is supposed to be purple.
During their fight at Autobot city, Megatron throws a rock at Optimus like a spear. Before he throws it it, looks big in his hands, but when it hits Optimus it looks quite smaller and fatter. Then Optimus pulls it out and it's back to the right size again. See more...
The creatures that judge Kranix, Hot Rod and Kup are later revealed in the next series of the Transformers cartoon to be the creators of all Transformers, and used to be the masters of them and Cybertron millions of years a go. They are called Quintessons. See more...
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Continuity: Towards the end of the movie, Spike and a few autobots are about to be dropped into the vat of acid. When the view is from above the vat, look carefully to see Daniel already in the room standing in the very spot he will shoot the cover from. However, a frame or two later shows Daniel running into the room.
Starscream: Who dares disrupt my coronation?
Galvatron: Coronation, Starscream? This is bad comedy.
Starscream: Megatron, is that you?
Galvatron: Here's a hint.
[Galvatron transforms into a cannon and obliterates Starscream.]
Galvatron: Does anyone else want to fill his shoes?