In the "steak experiment" sequence, Seth cuts the meat in two pieces, and teleports the bigger one. Later, Veronica eats a bit of this bigger half and finds that "it tastes like a steak", and when Seth gives her a piece of the smaller one and says "now try this teleported half", she finds that "it tastes synthetic". This is a continuity mistake. (It has been suggested that Seth deliberately misled Veronica as to which steak was teleported, to test Veronica's psychological reaction. However, this is unlikely; if the test were merely to determine Veronica's aversion to eating teleported meat, then it would not have led directly to the realization that the computer was incorrectly reassembling flesh).
When Seth brings Veronica to his lab for the first time, he is holding a padlock in his hand. We assume, since his experiments are secret, he locks the door when they are both inside. When she is getting ready to leave - after the tape recorder incident - the door is not locked when she goes to open it.
When the first baboon arrives in Telepod #2 he hits against the glass door of the pod, leaving a bloody mark. In a subsequent shot the amount of blood has significantly increased and the shape of the mark is different too.
When Veronica returns home to her apartment to unexpectedly find Stathis in her shower, and the camera begins to track and follow her down the hallway to the bathroom, the camera equipment and crew are reflected in the glass panes of the French doors.
In the last scene when Veronica shoots the shotgun, in real life it would have ripped away from her, and probably injured her hands and wrists. You must brace a shotgun to the body to prevent injury from the recoil.
When Veronica is playing the cassette tape of her recorded conversation with Brundel for her former boyfriend, the direction of the tape and the amount of tape left suggests that it just began from the beginning. However, the portion of the conversation that is being played is just before her tape recorder begins beeping, indicating that the tape is at the end and needs to be flipped over.
Every time Seth or any other creature for that matter goes through the teleporter, they're completely naked so as to avoid confusing the computer and introducing more foreign materials. However, at the end of the movie, Brundlefly shoves Veronica into the telepod fully clothed. Whilst the resulting merge of DNA would be human, it would in fact create a worse mutation due to there now being a combination of human, fly and clothing material merged.
Seth Brundle merges with a fly since a fly had flown into the telepod before transition. This would also mean that Brundle would merge with any other living object in the telepod including any bacteria living in his body and any virus currently in his body.
Additionally it has to be assumed that the baboon that transported successfully also had fleas on his body so the baboon also should be transformed into a baboon-flea-bacteria-mixture, not just a baboon.
When Seth is changing into a fly, he demonstrates how he can walk on the ceiling and walls like a fly. While upside down on the wall, he lifts his t-shirt to show the side of his body then places it back down. The reaction of the t-shirt to gravity (or lack thereof) made it obvious that he was filmed right side up and then the film rotated to get the effect.