Continuity mistake: 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.
Continuity mistake: 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.
Continuity mistake: 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.
Continuity mistake: 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.