Revealing mistake: In the scene where Ronnie visits Brundlefly for the second time we see Brundlefly walking on the ceiling and wall, however his shirt doesn't remain consistent with gravity. This is especially obvious when he pulls his shirt up to show Ronnie his new tumor and then places it back down. The shirt appears to be being pulled up to towards the sky from Ronnie's perspective.
Visible crew/equipment: After Seth Brundle has gone through his final stage of metamorphosising into the Brundlefly, he throws Ronnie (Geena Davis) into one telepod and then starts to make his way across the lab towards the other one. Watch as he emerges from behind a wooden pillar, there's one shot where a crew member's arm is seen reaching inside the back of the Brundlefly puppet, to move the creature's head. You'll need to slow-mo to see it but it's there. (As per the rules of this site, visible crew members is an acceptable use of slow motion.)
Continuity mistake: When Geena Davis gets kidnapped by the Brundlefly from the hospital, he gets into her hospital room by crashing through a plate glass window. When he leaves through said window we see that a portion of the left side has broken in half and is severely cracked. When John Getz's character attempts to stop them he smashes his hand through the same window section that's somehow become immaculately whole again.
Continuity mistake: When we see the first close-up of Stathis' dissolving hand, we see the fly vomit on his sleeve. In the next two shots of his hand, the vomit is gone. Then, when Stathis has fallen on he ground staring at the dissolved mess that was once is hand, the vomit is back on the sleeve.
Continuity mistake: When Seth cuts the steak in two pieces, one half is larger than the other. He then puts the larger half on the white and brown plate to teleport it. After cooking both pieces, he puts that larger half on the white plate. Seth then gives the smaller half on the white and brown plate to Veronica and tells her it's the piece that was teleported. Furthermore, when Seth cuts a very small piece from the larger half to give to Veronica, the next shot shows two remaining pieces on the white plate although only one piece should remain.
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?