When Megatron checks on Waspinator, the dinosaur head on his right hand switches to his left.
Starscream, as well as Unicron's planet mode, both if whom appear very briefly, look quite different from most of their former appearances. Unicron's ring is missing the "spokes" that connects it to his body, and Starscream's head is colored blue and white, instead of dark gray and black.
After Primal breaks free and attacks Starscream and Blackarachnia, the latter is missing her spider legs from her upper arms.
When Waspinator/Starscream is standing on the Maximal ship, giving commands, his leg clips through a cannon.
When Optimus Primal transforms to confront Starscream, the bottom parts of his cheeks are stretched down way too low, whereas his head sits extremely high. His lips don't move either as he speaks.
Blackarachnia calls the Decepticons their (the Predacons') ancestors. However she was originally a Maximal, and was only reprogrammed as a Predacon later on.