Continuity mistake: Marita Covarrubias tells the tribunal that she used to be Special Representative to the Secretary General of the United Nations. However, in "Herrenvolk," she told Mulder that she was the assistant to the S.R.S.G. (00:39:15)
Visible crew/equipment: In an early scene with Scully and Skinner talking in the hallway, there is a crew member obviously hiding behind a trash can. (00:07:10)
Other mistake: When Agent Comer is trying to steal the truck, he wants to hot-wire it. To do so, he unplugs the power and ignition wires in order to short-circuit them. When the owner unexpectedly appears, Agent Comer beats him up, steals the ignition key and starts the car with the key. The problem is that after unplugging the wires he cannot start the car with the key anymore. (00:20:40)
Character mistake: When Josepho meets Agent Scully, he recites to her the passage from the Bible that begins with the phrase: "Behold, a whirlwind came out of the north" Then he asks her if she knew that fragment from the Bible. She answers: "Ephesians." Unfortunately, she is wrong, because this fragment comes from Ezekiel 1:4. (00:30:30)
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.
Nothing Important Happened Today (1) - S9-E1
Character mistake: When Agent Dogget is eating breakfast, he listens to the information in TV news about "the body of 38-year-old Carl Wormus." However, the obituary which Agent Reyes is reading later says that "Carl Wormus was found dead at the age of 45." (00:07:30)
Continuity mistake: When Agent Scully is leaving her apartment to meet Agent Doggett and Agent Reyes, her mother is holding William in her hands. Depending on the shot, William's head is turned right or left. (00:21:30)
Continuity mistake: Agent Doggett holds the rubbings in his hands and after a while, he hands them over to Agent Reyes. However, when filmed from behind Doggett, the rubbings are in the same position in both situations. (00:07:45)
Continuity mistake: When Agent Doggett follows Lukesh into the parallel universe trying to find him, Lukesh suddenly reappears from Doggett's left and is pointing at him with the gun held in the left hand, while in the next shot he is aiming at the agent from his right holding the gun in his right hand. (00:03:25)
Dæmonicus - S9-E3
Revealing mistake: At the very beginning of the episode, we see the reflection of the Moon in a puddle. The Moon looks exactly as we see it in the sky. The problem is that in the puddle we should see the mirror image of the Moon. (00:00:05)
Trust No 1 - S9-E6
Revealing mistake: When Agent Reyes drives up to Agent Dogget's parked car, he looks in his rearview mirror. Its background should be obviously a transparent windshield to which the mirror is fixed. However, when the camera shows the image seen in the rearview mirror, we see in the background something similar in appearance to a solid wall. (00:10:50)
Continuity mistake: When Natalie stops kissing Dylan, her lips are covered with blood, but the moment she leaves Dylan's room she has no sign of blood on her lips. (00:32:00)
Nothing Important Happened Today (1) - S9-E1
Continuity mistake: When Agent Reyes and Assistant Director Brad Follmer meet in the bar, Brad is holding his glass either by the cup or the stem, depending on the shot. (00:18:20)
Trust No 1 - S9-E6
Continuity mistake: When the guy from the NSA is speaking with his supervisor, after the supervisor asks him about his wife and child, in the background he turns his head toward the supervisor, while in the next close-up take he turns his head toward the supervisor again. (00:12:30)
Trust No 1 - S9-E6
Continuity mistake: When Scully is pulling out, in close-ups she holds her cellphone in her left hand, while in distant shots she keeps her left hand on the steering wheel. (00:23:00)
Nothing Important Happened Today II (2) - S9-E2
Factual error: After a short examination of Shannon McMahon with a stethoscope and blood pressure meter Scully definitely claims that physically Shannon is absolutely normal. However, this type of examination cannot reveal any of Shannon's supernatural abilities. In order to prove or disprove that Shannon is a supersoldier, Scully could only examine if she could breathe underwater. (00:19:55)
Nothing Important Happened Today II (2) - S9-E2
Continuity mistake: After entering the room with the water tank Agent Doggett has dived into, the Assistant Director Brad Follmer screams "Doggett!", while in the same scene in the "Nothing Important Happened Today I" episode he screams "Agent Doggett!" (00:03:35)
Improbable - S9-E13
Revealing mistake: When Scully is examining the body of Vicky Louise Burdick, the dead woman moves her eyeballs. (00:22:50)
Trust No 1 - S9-E6
Revealing mistake: When Doggett visits Scully in Quantico and interrupts her pathology class, the cadaver left on the table blinks his eyes at least twice. (00:28:25)
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