Steeler and Grunt both make appearances in the movie. However, as per "Worlds Without End", they were left behind in the alternate Cobra-controlled universe and thus should not be on the active duty roster.
When The Joes are hiding the B.E.T. in the civilian base, Lifeline is seen standing on the truck. Lifeline is still supposed to be in the Himalayas, looking for Roadblock's unit.
Duke's chest injury alternates briefly when Falcon comes to his side. Serpentor's snake javelin clearly hit him in the left half of his chest, approximately where his heart would be, and his blood can be seen soaking his bandages. In one shot, the blood stain is on the right half of his chest, but in the next shot is back on the left.
Before Lift-Ticket tosses Falcon his parachute, there's a shot of Falcon already wearing one. It disappears when Falcon straps the chute that Lift-Ticket gave him.
After Duke is injured by Serpentor's snake javelin, Scarlett is seen holding his upper body up while he is tended to by Doc, holding his head in her hands. Although she is wearing gloves, part of her glove is missing, revealing a bare hand, but her glove is intact in the next shot.
The word "barracks" is misspelled as "barraks" on the side of a building within the G.I. Joe headquarters compound.
When Cobra Commander is seen in a chase for Serpentor's supposed assassin at the beginning of the film, he leads them in the wrong direction at one point. When he leads them away, his chest Cobra insignia is colored yellow instead of its usual red as seen in all the other shots in this scene.
Gung-Ho says it's time to go and Cobra says, "Straight head!", at which point Gung-Ho does a 360 and goes in the opposite direction.
In the opening scene, the tablet carried by the Statue of Liberty is clearly shown with the year of independence (1776) wrongly written as "MDCCIXXVI" instead of "MDCCLXXVI".