Visible crew/equipment: When Jeff Goldblum is first showing his telepods to Geena Davis, as the door to the first pod opens, you can see a reflection of a stage hand in the lower left corner of the pod door.
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.)
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.
PhixiusWe 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.