Plot hole: After less than 1 minute of investigation Scully found out that the photograph was bogus. It tells a lot about the "very best" specialists, mentioned by the Deep Throat later on, who had prepared the photo. (00:19:10)
Plot hole: The bugs are related to a type of mite, and when they are shown under a microscope they look like a glowing lice without wings. The problem is they are swarming in the air so they have to be able to fly - no way to do that without wings.
Answer: As he stated many times throughout the series, Mulder needed Scully to be sober and skeptical. Whenever Scully's skepticism wavered and she started questioning her own rationality, Mulder would try to restore her sense of skepticism, because he needed her to be clear-thinking.
Charles Austin Miller