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. (Time)

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. (Time)

Continuity: Unicron's head (specifically his forehead region) is drawn a bit differently during the 'transformation sequence' than elsewhere in the movie. This is likely due to the fact that this sequence was animated much earlier than the rest of the film, and changes were made to the character designs at this point. You can see a comparison image by following this link and scrolling down: http://tftm.net/errors.shtml.

Continuity: In the big battle scene, when Rumble starts to smash the glass, you can see Blaster transform in front of Perceptor. But when the shot changes, he is behind Perceptor.

Continuity: As Blaster makes the transmission there is a close up shot of all the Decepticons firing at the base. (Before Megatron notices the transmission) Look at Soundwave, and you'll notice his side facial panels are blue instead of grey. 2 shot changes later and they are back to the right colours. (Time)

Continuity: When the Decepticons shoot the autobots in the shuttle, at the early part of the movie, Ironhide's position after he has been shot changes. First he is lying down on Megatron's left, but when he makes a grab for Megatron, he has somehow got to Megatron's right.

Continuity: There is a shot of Unicron firing pink/purple lasers from his eyes as he stands on Cybertron, but when the shot changes to a close up of his face the lasers have changed to a blue colour. (Time)

Continuity: When the Decepticons get into Astrotrain, there is a sort of semi-circle shaped space to get through, but when it shows Astrotrain's door closing, there is no semi-circle, just a big space.

Continuity: When Perceptor scans the Decepticons at the near start of the movie, you get to see the view from a shot inside his scope. However, he lowers the scope down after he has finished. But when the shot changes the scope is still up looking at the Decepticons. (Time)

Continuity: 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.

Audio problem: When Kup and Hot Rod are smashing up the Sharkticons, Kup says something, (I think it's after he rips the tail off one of them), his mouth doesn't match what he says.

Continuity: When Unicron first tortures Megatron, there is a shot of Megatron in pain, and he is missing his Decepticon symbol on his chest. It was on before and does come back a shot later. (Time)

Continuity: When Ratchet gets shot in the shuttle attack scene, the red cross on his arm vanishes.

Continuity: In the scene where Blaster tries to communicate Prime, the dome on Blaster's head doesn't know if it wants to stay red or white, it switches repeatedly.

Continuity: Unicron's left eye is smashed when a ship goes through it, but when the Dinobots attack Unicron there is a shot of them flying up to his head and his left eye is intact. (Time)

Continuity: When Soundwave's cassette robots first land on the glass (where Blaster makes the transmission) both Rumble and Frenzy's eyes are coloured grey instead of red. (Time)

Continuity: At the end of the movie, there is a pan from left to right of all of the Autobots, and Blurr and Perceptor are both missing their Autobot symbols. (Time)

Other: The credits for the movie say that they are in alphabetical order, but Peter Cullen is listed before Scatman Crothers.

Continuity: At the very start of the movie, when the robots see Unicron coming towards them out of the window, if you look at the bottom of Unicron, his ring is shown in front of a building, instead of behind it.

Continuity: When Hot Rod goes next to Prime and says "Optimus....forgive me," the aerial things on the side of Prime's head are grey instead of blue.