Executive Meddling: Originally pitched as an independent gross-out comedy in the vein of Pink Flamingos, the studio forced the makers to deliver a PG-13 movie. The original script was a lot filthier, and many of the freaks had to be rewritten or cut out completely. For example, the 'Human Flame' was originally written as the 'Human Bong'.
Also, they made the filmmakers change the name of the movie from Hideous Mutant Freekz to Freaked, which Alex Winter and the director hated because it sounded too much like Tod Browning's Freaks.
The studio also dumped the film into a few theatres after they realized it wasn't anything like the Bill and Ted movies.