When Bulkhead breaks Ratchet's tool loose, the metal panels on the right side of his abdomen sink into each other.
As Starscream's bomb bounces off the Energon crystals, parts of it seem to disappear, even though they are not obscured by the crystal. The 'motion blur' effect added onto the crystals apparently blocks out the bomb's underside completely, even though it should be partway visible behind it. Thus it looks like parts of the bomb disappear and then reappear as it bounces.
In one shot, as the assembled Autobots are firing their weapons at the Decepticon drones, Bulkhead's large left forearm very clearly passes into the crate he's hiding behind.
In most scenes, the lip-sync is noticeably off. For example, when Optimus Prime talks to Agent Fowler ("Perhaps you can condone widespread human casualties..."), his lips move in a totally different manner that just barely mimic the words he's saying.