- Some international video and television versions omits several musical cues from the soundtrack including a moment where Jerry Goldsmith's score accompanies the Mr. Ed theme sung by Wak and the 80s music Wak listens to on Darren's Walkman (in these versions, you can't hear the music at all). Several score cues are also missing aboard Wak's spaceship and in the first third of the film. It is unclear where this is a mastering issue or a music rights issue.
- The shorter version released on home video as "A special home video version of Explorers", actually contains a scene which does not appear in some theatrical versions. In this scene, Ben falls asleep in class and finds himself in a dream where all his classmates have disappeared. With his glowing gift from his alien friends in hand, he rises out of his seat to find the Thunder Road in the corner of the classroom looking brand new. (It had fallen into the lake while returning home after their visit with the aliens.) Ben then finds himself flying with Wolfgang, Darren and Lori.
- The original cinematic release includes another small scene deleted from the movie. After Ben, Wolfgang and Darren have decided the Tilt-A-Whirl they found in the junkyard is an appropriate shell for their spacecraft. The scene that follows it has the boys pushing the Tilt-A-Whirl to the top of a hill and chasing after it frantically as it rolls down the other side. It rolls off of the street and lands in the ditch that runs along the Mueller property. The movie resumes with the boys pushing it farther along down the ditch until it comes to rest near the Mueller house.
- The home video and cable television versions are re-edited by director Joe Dante and are two-minutes shorter than the original theatrical release. One of the missing scenes from the home video release has Ben [E. Hawke] and Wolfgang [R. Phoenix] walking to school and discussing the strange dreams Ben has been having. Ben then shows Wolfgang the circuit diagram drawing that he dreamed the previous night. Wolfgang then offers to input the diagram into his Apple IIc computer. The two then start talking about the school bully Steve Jackson. It's here when we first hear Ben comments/mention, quote: "Steve Jackson has elephantitis of the ego!" This is the reason why Ben is later punched by Jackson in another scene. The music on the soundtrack album called "Sticks and Stones" is about two minutes and this is the music which accompanies the missing scene.
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