The Autobot Matrix of Leadership is nowhere to be found on Prime's chest when Wheeljack and Ratchet are repairing him.
The colors of the three Seekers (Starscream, Skywarp, Thundercracker) keep changing randomly in the opening scene. For example, when Skywarp teleports, he disappears in Starscream's color scheme, and when he reappears, he is colored like Thundercracker.
Due to a mix-up in animation models, the green-uniformed human soldiers protecting the weapons factory in one shot turn into hard-hat wearing factory workers in another shot.
When the Autobots are shown talking to Optimus, and later arriving at the factory, Bumblebee is the only yellow Autobot shown. However, when the Autobots transform to go to the factory, Sunstreaker is shown transforming instead of Bumblebee.
When the Autobot away team races back to Shockwave's tower, Ironhide is painted with Trailbreaker's black and gray colors, making him resemble a Diaclone incarnation of his toy.
The nitrogen pack that Ironhide uses in Shockwave's control center is labeled "NITRGEN" (and Ironhide shouldn't have to use a pack anyway, since he has a built in liquid nitrogen projector).
Rumble blinks out for a few moments when the Autobots arrive at the Space Bridge. You don't need to watch this frame-by-frame to notice it.
As Shockwave and a Reflector soldier unload the Space Bridge's shipment of Energon cubes, the Energon is not filled with an illumination effect, and appears as solid black bars. In an earlier scene, this lighting effect is also mismatched with the animation of the characters, and you can see the black Energon cubes that are supposed to be brightly colored.
Because the background art moves around to simulate a camera tilt, the foreground animation of Prime's trailer receding into the background looks instead like it is shrinking into nothingness in midair.
There's a big S-shaped hair in the center of the screen as Wheeljack describes his shop on Cybertron.
At the Space Bridge site, the camera pans across the scenery, but a painted foreground tree travels with the move, making it look like the tree is mobile.
When Starscream reacts to Optimus Prime barreling into the factory, his voice is not electronically enhanced.
Optimus Prime's mouthplate moves when Megatron concedes defeat.
It is doubtful Brawn wouldn't notice a cassette-tape (that is really a Decepticon spy in disguise) dropping onto his shoulder as he walks.
It is unclear how Chip knows Skywarp's missile is a heat-seeking missile before it does anything to suggest such.
Chip is not harmed at all by the acid rain.