When Invisigoth takes the phone from Scully and hangs up on Mulder, he is left talking to a dial tone. Because they are using cell phones, there would not be a dial tone after one person hangs up.
When Mulder is approaching the travel trailer with the A.I.'s memory banks, he is following just a fiber optic line. With all the equipment on board the trailer, it should have had larger power cables running to the trailer.
In the diner, supposedly active and open, not a single wait person comes in to serve the multiple customers who have entered. Nor are they injured in the ensuing massive gun battle.
Mulder points out that the U.S. Marshalls were killed with teflon-coated bullets, implying that that was the reason that their Kevlar vests did not protect them, yet a Teflon-coated bullet does not have any extra ability to penetrate body armor than a normal bullet. In the 1980s and '90s, some anti-gun groups claimed that a teflon-coated bullet could penetrate kevlar vests, leading them to be called "cop killers," but in fact that was a completely false statement. Teflon is a synthetic polymer that has anti-friction and lubrication properties. The polymer was added to bullets to reduce drag and friction while the bullet traveled through the barrel. The coating also reduces bullet ricochet. Some groups claimed that because the bullets had less friction and better lubrication that made it possible for them to penetrate Kevlar vests; however that was a completely unfounded claim. This misconception is also often shown in TV and film.