During the fight scene with Mulder and Bear, there is a running pinball machine in the background. When the machine is visible for the third time, it has been powered off. Throughout the rest of the episode, the machine remains on.
The video transmission recorded by Richter is clearly not the footage watched by Mulder and Scully later on. There are obvious differences in Richter's way of speaking that reveal that the two versions were two different takes.
A close-up of the mysterious worms obviously consists of real life meal worms. The CGI worms seen in several shots look very different, lacking the clearly segmented exoskeleton, limbs and abdomen/thorax/head transitions.
(at around 2 mins) The agents arrive at what is called "Doolittle Airfield Nome, Alaska". There is a Nome airport, and the smaller "Nome City Field", but no Doolittle Field in real life.
FBI Agent Scully makes two critical gun safety mistakes:
When she dramatically removes the magazines from her Sig and Mulder's Glock automatic pistols and throws them out in the snow, she fails to remove the chambered rounds, meaning the guns are still loaded.
Scully also fails to unload the pistol she sealed in an FBI evidence bag, and the deranged Nancy later fires a round from it.