In one scene where Cobra Commander is discussing Shipwreck, the Commander is wearing his blue hood. Rising from the table, he is suddenly wearing his silver battle mask and then, once at the door leaving the room, is back to wearing his hood.
When Shipwreck has the flashback of his first encounter with G.I. Joe (The Revenge of Cobra), he's piloting his sand skiff with Flint and Snake-Eyes as his passengers, even though it was Flint and Mutt. The sand skiff also was changed from some green material to ordinary wood.
When Shipwreck knocks out the nurse by drugging her with the milk she has black hair, after he puts her to bed and gets dressed, her hair is blonde.
At the 19:49 mark, Roadblock's mouth moves along with Prof. Mullaney's for a couple of seconds.
The Crimson twins insist that Cadet Deming handles the interrogation of Shipwreck. When the twin on the right side of Cadet Deming says "essential to her training," his mouth doesn't move.