Continuity: At the end of "The Traitor, Part 1", Duke is put in a coma that he does not come out of until the end of part 2. However, when the GI Joe grunts are seen scaling the arena walls and begin attacking the Crimson Guard Commanders Xamot and Tomax, Duke can clearly be seen climbing with the grunts and diving on top of the twins.
Continuity: When the Joes and the Oktober Guard are seen riding sleds in "The Great Alaskan Land Rush", Scarlett is seen riding with Duke while Roadblock is seen riding with Diana of the Oktober Guard. In the next shot, however, Roadblock is suddenly with Sgt. Horrorshow.
Continuity: When the Joes and the October Guard are seen riding sleds in "The Great Alaskan Land Rush", Scarlett is seen riding with Duke while Roadblock is seen riding with Diana of the Oktober Guard. In the next shot, however, Roadblock is suddenly with Sgt. Horrorshow.
Revealing mistakes: In "The Captives of Cobra, Part 1", Scarlett's real name is revealed to be Shana M. O'Hara. However, when her name comes up on the Cobra computer screen, her surname is misspelled as O'Hala.
Continuity: Gung Ho's hat disappears and reappears randomly when the Joes raid the arctic Cobra base in "The Viper Is Coming".
Continuity: Whenever Cobra Commander wears his hood, we see his (clearly) human eyes and eyebrows. However, as shown in G.I. Joe: The Movie, the Commander in actuality has blue skin and reptilian-like eyes as a result of being mutated by spores.
Continuity: Midway through "Cobra's Candidate", Storm Shadow tells Buzzer that Cobra Commander has sent him a communique about the pep rally, to which Buzzer replies "Come on mate; Cobra Commander knows I can't read." Per his file-card, however, Buzzer was a college professor prior to becoming a Dreadnok, and as such would most certainly know how to read.