The first videotape of Seth Brundle (Jeff Goldblum) (where he theorizes that the teleporter improved him) is actually part of a deleted scene from The Fly (1986). The scene was slightly edited for this film, and Veronica's (Geena Davis) voice was dubbed over by Saffron Henderson (who plays Veronica at the beginning of The Fly II (1989)).
The Telepod props from The Fly (1986) were destroyed after filming was completed and had to be rebuilt.
Chris Walas wanted Geena Davis to reprise her role as Veronica Quaife for the birth scene at the beginning of the film. Geena Davis declined, because she had found the maggot-baby dream sequence in the original film emotionally upsetting and was replaced by Saffron Henderson, despite being 10 years younger than Davis.
The green flashes of light between each credit in the title sequence were actually borrowed from an alternate, unused title sequence for The Fly (1986).