Other mistake: While Cadet Hayes is being interrogated, he says, "I studied the photos of your son's death. They called to me. I don't know why, but it was a message and I listened." Then Scully answers, "And then you killed Agent Doggett's son." This answer is illogical and complete nonsense because the photos of Agent Doggett's son were taken after his death. (00:36:05)
Other mistake: When Doggett starts clawing at the freshly plastered wall, he does so at just below his eye-level and blood starts pouring from the hole he makes. The dead woman inside the wall was stabbed in the lower abdomen; there's no way that blood from the abdominal wound would've seeped through the wall at the level he was digging.
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