According to Wil Wheaton, in the scenes that he was in with Robin Williams, they would film a take the way it was supposed to be filmed. After that take, Williams would often want to improvise scenes differently than the script, just for fun. Those scenes were not added to the actual film, but there were enough scenes to make an entirely different movie.
During late 1993, when this movie was first announced, Steven Spielberg considered being the Executive Producer of this film, and have the film released under the Amblin label. But he decided not to go through with it, because his only choice for the lead role, Robin Williams, was, at the time, in a bitter fallout with the Walt Disney Company, and refused to be in the film. John Hughes' first choice for the lead role was always Williams. He lined up some other choices including Christopher Lloyd, Jeff Goldblum, John Lithgow, Tim Allen, and Sir Patrick Stewart. As soon as Williams made peace with the Walt Disney Company, Hughes immediately cast him in the lead.
Early in pre-production, Steven Spielberg considered producing this movie. When Professor Brainard takes Sarah for a ride in the T-Bird, he flies through a cloud in front of the moon. As the cloud disperses you can see a reference to E.T.: The Extra-Terrestrial (1982), which was directed by Steven Spielberg.
Sound Designer Andrew M. Somers created the sound of Flubber, by using a rubber balloon filled with water, Metamucil, and air. The Metamucil became "gloopy", and in the balloon, it helped make a rubbery, gurgly sound. The voice of Flubber was performed by Scott Martin Gershin, and was processed to raise the pitch to sound small and squeaky.