Ultra Magnus was suppose to die in a different way at first. The sweeps fired long laser beams that looped round him, and then they all flew off in different directions, ripping Ultra Magnus apart. Censors forced the artists to change it since it was to violent for a kids movie. However, you can still see the Sweeps fire the long laser beams, but when the shot changes lots of little laser blasts his Ultra Magnus. See more...
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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.
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.
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.
Continuity: In the scene where Hot Rod and Kup are stuck underwater, we see Hot Rod fighting a Giant Squid. Just after the Giant Squid swims off we see a shot of Kup lying on the ground with his right arm and his left leg missing. However, when Hot Rod gets to him they have swapped sides, the left arm is missing and the right leg is missing (don't be confused by the fact Hot Rod flipped him). Only two of Kup's parts are missing, as we only see Hot Rod pick up two parts.
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: During the fight scene between Optimus Prime and Megatron at Autobot City, Megatron pleads for mercy. He reches for a gun that is under some metal. The gun is black in colour. Then Hot Rod jumps on him, Megatron stands up and the gun is now purple. It then goes to a close up of Megatron with the gun in one hand, and Hot Rod in the other, and the gun is now black again.