The movie's opening sequence with the G.I. Joe soldiers saving the Statue of Liberty from the Cobra invaders was originally intended to be the climax in the earlier drafts. The director and storyboard artists decided to salvage it and turn it into the film's opening, so newcomers could understand the premise of the series and to justify Serpentor shouting at his underlings in the following scene as in the final drafts of the script opened on Cobra Island with Serpentor shouting at them for no discernible reason.
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.
The movie was being produced by the same company, and at the same time, as The Transformers: The Movie (1986). This 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 movies, 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. However, according to story consultant Buzz Dixon, if you watch the "Duke goes into a coma" sequence with the volume turned down, it's obvious that Duke actually dies at the end of the scene.
The name "Cobra-La" was not intended to be in this movie. The writers planned to replace this when they came up with a better name, but Hasbro loved the name.
Jinx makes a reference to having a blind ninja master. This Blind Master appears in the G I. Joe comics published by Marvel Comics.