Continuity mistake: During the meeting at a horse track, after the CSM says "You need my expertise, " the First Elder raises his head. In the following shot from the other side, he raises it again. (00:21:00)
Continuity mistake: When Mulder and Scully talk about the piece of skin while driving to the reservation, one can see that there are green trees from the Mulder's side of the road, but when the shot is taken from the outside of the car, there are only grey bushes and landscape devoid of nearby trees on both sides of the road. (00:07:00)
Continuity mistake: When we see Dana Scully after being abducted she has an instrument in the middle of her stomach, inflating it. When we see it in the first shot there is nothing but the instrument, then in the next shot there are gauze pads taped down all around it.
Continuity mistake: When Mulder tells Krycek to go to the bathroom and clean off, in the front shot Krycek holds his right hand raised, while in the back shot his right hand is lowered. (00:42:10)
Invocation - S8-E5
Continuity mistake: When Scully finishes her conversation with Doggett and walks away, there is only one dark-haired policeman watching the crime scene, but when Doggett looks at the crime scene and Mr. Underwood gets up, there is a blond-haired policeman talking with someone. (00:41:55)
Via Negativa - S8-E7
Continuity mistake: When Doggett and Skinner visit Dr. Andre Bormanis at his place, in the first shot from the back he is leaning over some laboratory gear that is holding in his hands, while in the next front shot he is standing upright manipulating on the table with his hands. (00:18:10)
Via Negativa - S8-E7
Continuity mistake: When Doggett leaves his office, he reaches for his coat, grabs it and starts to put it on. In the next shot, when Langly, Frohike, and Byers look in Doggett's direction, we again see that he takes the coat off from the chair. (00:27:55)
Within (1) - S8-E1
Visible crew/equipment: When Scully is looking at her reflection in the mirror, the camera moves toward her and its shadow appears on the left side of the mirror's frame. (00:02:00)
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)
Continuity mistake: When Knowle Rohrer is talking with Agent Doggett face to face in a separate room about the super-soldier project, he is wearing a red FBI badge, but in the previous scene when he came to visit Doggett, he was wearing a regular FBI badge. (00:08:40)
Continuity mistake: When Agent Reyes and Agent Scully are talking about mood music, in some shots Reyes rests her hand on the bed's backrest, while in other shots she firmly grabs it. (00:14:45)
Continuity mistake: When Agent Reyes is aiming at the oncoming car of a ranger, in the front shot the windscreen of the car is completely covered with dirt and fully opaque, while filmed from the ranger's side the windscreen seems to be transparent and relatively clean. (00:17:00)
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)
Trust No 1 - S9-E6
Continuity mistake: When Scully reads the alleged printout of the email sent to her by Mulder, it says: "Dearest Dana: I've resisted contacting you for reasons I know you appreciate...I want to come home, to you, to William", but when Scully has previously viewed this message in the internet café, it had a different form: "I've resisted contacting you for reasons I know you continue to appreciate...I want to come home. To you, and to William." (00:06:05)
Visible crew/equipment: In the final scene of the episode, when the camera goes up, its shadow can be seen on the left side of the screen. (00:42:15)
Plot hole: When Arthur wakes up on the bus, he sees an alien reflection in the window beside Josh, but it's not possible that the reflection could be seen at all - especially from the angle that Arthur first sees it - considering how much of the pillow is covering both Josh's face and the window. The pillow extends past Josh's face so he could lean on it as cushioning against the window, but somehow Arthur sees a full facial reflection.
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