Mindful that the TV show was being compared unfavorably to "Robotech" (1985) for its sanitized depiction of combat, the producers decided to have a death scene for Duke to give the movie a harder edge, but upper management forced them to add a line saying that he only went into a coma.
The character of Big Lob was created for the movie, there is no action figure of him, nor is he in the comic books.
During the opening sequence when Pythona is breaking into the Cobra base, the audio during the part where the snakes chew the fence open is sampled from the climactic lightsaber duel between Darth Vader and Obi-Wan Kenobi from Star Wars (7 minutes and 2 seconds into the film). Additionally, during the scene where Cobra first attacks the Joe's secret base, which holds the B.E.T, more audio from Star Wars can be heard, including OBVIOUS TIE Fighter and even breathing sounds from Darth Vader's suit, when Duke is attacked by Serpentor (roughly 15 minutes and 43 seconds into the film). This particular piece of audio is taken from the scene in Star Wars where Vader is defending the Death Star, as you can also hear the instrument panel beeps from his TIE Fighter.
The movie was being produced by the same company, and at the same time, as The Transformers: The Movie (1986). It had been agreed that both movies would suffer the loss of the lead heroes, Optimus Prime and Duke. Production had begun on G.I. Joe first, and was thus expected to be released first. During the production of the two films, G.I. Joe Got held up while Transformers finished production. Release dates were changed and Transformers got a theatrical release in 1986. Optimus Prime's death sparked some controversy and caused the writers to change Duke's death to a coma. G.I. Joe never got to the theaters, and was released to video instead. Had G.I. Joe been released first, Optimus Prime might have survived the movie.
The name "Cobra-La" was not intended to be in the movie; the writer's planned to replace it when they came up with a better name, but Hasbro loved the name.
Several scenes were storyboarded but never animated. One featured reaccuring character Hector Ramirez reporting from the UN after the spores are launched into orbit. Another scene featured Jinx with her blindfold on and holding a sword, trying to stop the Thunder Machine from escaping with Serpentor. Falcon sees her and pushes her out of the way. She starts to argue with him but then they notice smoke coming from the stockade. The scene then leads into Falcon running into Hawk.
Lt. Falcon was originally intended to be the son of General Hawk.
This was to be feature-length theatrical release. The box-office failure of Sunbow's earlier films "Transformers: The Movie" and "My Little Pony: The Movie", this resulted in the Joe movie going direct to video and TV.
The film's opening sequence with the GI Joe soldiers saving the Statue of Liberty from the Cobra invaders was originally intended to be the climax in the earlier drafts.
When Sgt. Slaughter uses the term "ditty bag" to illustrate Lt. Falcon's pass or fail. DITY is military jargon for a "Do It Yourself" move; when a soldier out-processes from an installation for discharge or another assignment.