Plot hole: The whole problem with the teleporter occurs when fly DNA is mixed in with Seth Brundle's DNA, starting his transformation into the Brundlefly. Brundle is on a hiding to nothing from the word go, and the fly is irrelevant. Humans are a walking talking mass of foreign DNA - we are host to one trillion bacteria all of which has a complete complement of DNA, as do various tiny mites that live in our hair follicles and all sorts of single cell organisms in our gut. If the transporter serves to mix the DNA of all living creatures which are in the transporter pod at the time Brundle would turn into a half-man, half-bacteria. Incidentally, DNA from a bacteria, an amoeba or a hair follicle mite would be just as 'compatible' with human DNA as that from an insect. It's quite a simple chemical, really.
Factual error: There is no possible method of "fusing" the genetic material of a common housefly (Musca domestica) and a human. The housefly has twelve chromosomes, humans forty six. There is no way to combine the two in order to produce a viable organism. Thirty four of the human chromosomes would have no matching chromosome to "fuse" with, meaning the physical characteristics coded by those genes would not form. The Brundlefly would be missing three quarters of his human body.
Suggested correction: There's no possible way of teleporting physical objects either, but it happens in this movie. This is science fiction. These kinds of "factual errors" are not valid.
The film presents no scientific explanation for "teleportation" but does for "genetic merging." Teleportation is possible in this film's universe, but "genetic merging" is impossible in any universe.
Genetic merging is possible in this film's universe; that's the whole point. It doesn't matter if the explanation doesn't stack up, it still works.
Trivia: An extended ending showed Geena Davis dream about giving birth to a baby with butterfly wings. This was cut from the film to emphasize the drama of Seth's death.
Suggested correction: Actually, the 'butterfly baby' endings were cut for two primary reasons: the stop-motion animation of said baby was a rushed job that didn't look particularly great, and both test audiences and the crew alike voted against the two endings where Veronica ended up with Stathis (even Stathis' actor stated, 'there's no way she'd get back together with him after that'), while the two where she ends up alone but happy felt at odds with the rest of the movie's tone.
Suggested correction: Being as how the bacteria and mites and such were IN or ON Seth, the machine was able to organize those symbiotic relationships accordingly as teleporting one would teleport all. The fly was separate, not touching. The machine was not programmed to anticipate two separated entities and so combined them into one on the other side.
Phixius ★
We leave behind a vapour trail of bacteria and viruses (among other things) as we walk, in our breath and emanations from pores in our skin, and Brundle isn't trapping any in his clothes as he isn't wearing any. Brundle has an invisible cloud of DNA floating around him in that teleportation chamber and as far as the machine is concerned their DNA has exactly the same status as that of the fly.