At the beginning of Nemesis part one while Optimus is reading, behind him you see Black Aracnia and you clearly see Cheator, but not in his trans metal 2 form - it is his previous trans metal form.
When Optimus is reading the Covenant of Primus, behind him Transmetal Cheetor is carrying a crate. By now however, he was in his Transmetal 2 form.
It is evident that after his comrades blow him up, Waspinator's head doesn't land on the rock, but actually floats in the air. We can see the underside of his head, which wouldn't be possible if it really rested on the rock.
The explosion that tore apart Silverbolt left both Depth Charge and Optimus Primal undamaged, yet they were not any farther away from the bomb than Silverbolt. In fact, Depth Charge was standing at ground zero, but hasn't been damaged in the least. Interestingly enough, all of the characters in the scene seem to be worrying about Silverbolt, seemingly ignorant of the fact that he wasn't the only one to be caught in the explosion.