Plot hole: At the end, a man is attacked while standing in the light of his automobile's headlights. Supposedly, though, the bugs were terrified of light.

Continuity: When they find the felled ancient tree, the stump that Mulder clambers up onto to investigate the growth rings has a distinctive crack at the center and the growth rings are irregular in shape. However the stump that we get a close up of has no crack and regular circular rings.