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.
Plot hole: In any given volume of air, there are any number of tiny, living organisms; dust mites, viruses, bacteria, etc. Why did the teleporter combine Seth's DNA only with the fly that was in the chamber? If he had taken the "floating organisms" into account in his calculations and programming, then why would he not have excluded ALL foreign DNA?
Suggested correction: Just because a character doesn't do something that they probably should/could have, it doesn't make it a plot hole. It's arguably a character error.
The correction makes no sense. If the teleporter included the fly's DNA, it would also have included the DNA of - literally - trillions of bacteria, viruses, mites, etc., etc., that are in and around Seth's body. You cannot have it both ways.
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.
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.
We don't know enough about how the machine works to determine how it might differentiate different DNA types. Unexplained science means it's somehow able to do it. Willing suspension of disbelief for the win.