A lot of the scenes with the Beta Unit were shot after main filming was complete because the test audience liked the comic relief of the Beta Unit scenes and the director decided they added more originality to the "boy gets to go to outer space" story. This is why in many of the Beta Unit scenes Lance Guest is obviously wearing a wig - he had cut his hair by the time those scenes were shot.
Robert Preston and Dan O'Herlihy had never met before this movie. When they finally met on the set, O'Herlihy was already in Grig makeup with a full-head mask. O'Herlihy introduced himself and Preston jokingly replied that of course he recognized O'Herlihy because he had "one of those faces."
Although Wil Wheaton's speaking scenes were cut, he can be seen in two scenes - running around the trailer park early in the film (wearing a red football jersey), and in the final scene, where he is obscured, standing behind Louis (wearing a blue jacket, possibly over the red jersey).
Atari actually programmed games for its 5200 SuperSystem and 400/800 series home computers as a tie-in with this movie. The games never went past the prototype phase (though copies do survive). Also, the game was nothing like the arcade machine Alex played in the film - the technology did not exist at the time to produce real-time 3-D polygonal graphics on a home machine. Rumor also has it that Atari produced one prototype Last Starfighter arcade machine, but it since has been lost. An early Atari 2600 program was revamped into the game released as "Solaris".