Absentee Actor: Frank Oz was unavailable for most of the filming. In his absence, Miss Piggy was performed by Peter Linz (and Steve Whitmire in at least one scene), Fozzie and Sam were both performed by John Kennedy, and Animal was performed by Rickey Boyd. Oz looped his characters' voices for the scenes for which he was not on the set.
Creator Backlash: Frank Oz went on record to say that this "was not the film we intended to make." It would be the last Muppet film with which he is associated.
Creator Killer: The failure of both this and The Adventures of Elmo in Grouchland badly damaged The Jim Henson Company's film division Jim Henson Pictures and prompted Columbia Pictures to drop the label. While Henson did manage to produce more theatrical filmsnote Albiet with the JHP name only appearing in the credits until 2005, they never made another one with the Muppets, and the next time they graced the big screen, Disney handled it solo.
Deleted Scenes: Pepe announcing that the kitchen is "closed" during the breakfast scene.
Rizzo visiting Gonzo on the roof of the Muppets' house, and trying to talk him into coming inside.
Prior to that, it was going to be MuppetsinSpace; aliens would've abducted Kermit because he resembled their leader, forcing the other Muppets to journey into space to rescue him. Though this was announced first, it was passed over in favor of the movie we got; Welch's Jelly jumped the gun and released collectible jars based on the ultimately-unmade movie.
The film was originally going to be an actual musical, with the song "I'm Going To Go Back There Someday" from The Muppet Movie making its return, this time, in reference to Gonzo's ambition to find his family. Then someone said, "Naaaaah! 70's funk!"note It is on the soundtrack album, though.
The rock band Ween wrote an Image Song for Gonzo, entitled "Eye 2 The Sky". According to IMDB, they sent it to the people making the movie around the time the "70's funk" decision was made, and were then asked to do a cover of "Brick House", to which they declined. (The original Commodores recording plays at the beginning of the movie.)