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.
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.
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.
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.
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!"
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."
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.
Plot hole: After Exley has gotten up after being hit by the ball, Dales notices green alien blood inside the glove where the back of Exley's head was resting. However, Exley was hit in the face, not the back of the head; not only was there no bleeding face wound while he was on the ground, but the glove was clean when Exley first gets up.
Plot hole: When Arthur looks closely at the green alien blood on the baseball glove, he has no reaction to it, despite the continuous pattern in the show about the blood being incredibly toxic to humans, even from a distance. It should have badly hurt his eyes at the least.
Other mistake: When Mulder is on his knees in the cafeteria talking to the gunman, there are several shots where you can see the sides of his jacket hanging wide open because of his raised arms, which would make the gun on his belt easily visible to the gunman as he talks to him, but he somehow doesn't see it until he goes to take Mulder's phone.
Continuity mistake: When Scully enters her apartment, the blinds are up and there is quite a lot of light in the room. However, when the flashback with Mulder ends, during which Scully was supposedly standing still, the shades are rolled down and there is much less light in the room.