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.
Continuity mistake: When Danny & Debbie are having their New Year's dinner at home, the champagne foam instantly disappears in the very next camera angle after pouring it.
Visible crew/equipment: When Charlie walks down to the front of the class in the hanger, Jester is the only one at the front. Look at the reflection of Maverick's glasses, and the reflection shows lots of people standing in front of him, likely film crew. (00:26:20)
Factual error: During most of the basketball games, you can see an American flag in the background. This is not the problem, the problem is that it is hung wrong, the stars should always be on the top LEFT not RIGHT.
Visible crew/equipment: Near the beginning of the movie there is a brief scene around the empty house. While the camera is in the kitchen you can see a reflection of one of the set guys moving in the fridge handle.
Continuity mistake: When the boys are dunking each other in the swamp Gordie starts to wade away, when he passes the camera his hair is dry but when he reaches the bank it's wet again. (01:04:56)
Continuity mistake: When William Petersen is talking to his kid in the supermarket, the cereal boxes behind him on the shelves change between two shots. The items behind Kevin also change during the scene. (01:09:05 - 01:10:20)
Continuity mistake: There is a scene where Molly Ringwald is confronting her father about lying about seeing a counsellor. His hair is sweaty and messed up a bit and then it changes position to Molly Ringwald and back to her father. Then you will notice that his hair is combed.
Continuity mistake: In the scene where Bunny kills the one legged Vietnamese with the butt of his gun, watch the cigarette in Sgt. O'Neill's mouth. In a shot after the kid is dead, the cigarette in O'Neill's mouth is short. When it shows him again, the cigarette has mysteriously grown. (00:50:00)
Continuity mistake: The cave bear tears the head off the man with the blue eyes. In the very next shot there is no trace of blood anywhere on the bear.
Continuity mistake: Early on Nancy is in a limo and a man with long hair tells her to get drugs. While he's talking his hand goes from resting on his chin to resting on the armrest instantly.
Revealing mistake: In the opening scene the camera pulls back from a bedside locker to an over the shoulder shot of Kathleen Turner doing her make up in the mirror. Close inspection shows that the shoulder in the foreground is actually that of a double who doesn't quite match Turner's movements.
Factual error: Right before Frank humiliates Dorothy for the first time, he blows out one of the gaslights in her apartment. That is never done in real life, for the same reason you would not blow out the pilot in your stove.
Factual error: Calendar date at the very beginning of the film (in the police station), shows the dates of Saturday 20th/Sunday 21st July 1983. However the 20th and 21st July 1983 fell on Wednesday and Thursday.
Continuity mistake: When Tiger and Fievel are doing their musical piece, Tiger wipes off the mirror and they appear the same size. When he lays out in front of the mirror, singing the line "We'll be there to pick each other off the floor", he places his head next to the cage bottom, still laying on the floor between them. In the mirror, however, that cage bottom is not reflected at all. (00:57:30)
Continuity mistake: Hook's earring appears, when he talks to Crissy by the fridge after her late night out.
Factual error: Cruise is breaking and if you watch the eight ball after the break it's following the 5 into a pocket at the end of the table closest to Tom. Now the 8 ball didn't necessarily go in because they focus on the one ball, but in the next frame shot, there's no way it could be at the opposite end of the table like they show. (00:29:20)
Plot hole: Sarah breaks a mirror in frustration by throwing something against it. Then she buries her face in her arms and sobs. It remains a mystery how she managed to cut her hand so bad that it needed to be fixed with five stitches, as she isn't even seen picking up the pieces. (00:59:15)
Continuity mistake: During Kevin Bacon's race with fellow messenger, the scenes shift back and forth from New York to San Francisco. In one city, he's on a fixed gear (no freewheel on back wheel) and when the race is taking place in the other city, he's riding a single-speed. Basically, the cityscape and bicycles switch from scene to scene.
Factual error: The movie they're watching in the theater, "The Fly", is shown backwards. The first scene they see should have happened after the last scene they see.
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.