Factual error: When the Smoking Man comes back to the base, in the first shot the tracks are shown, but they definitely do not belong to his snowcat but Mulder's. Only Mulder's snowcat has triangular-like shape of the tracks. (01:33:05)
Revealing mistake: Near the beginning as the helicopter arrives to take the boy away, a man steps on a tumbleweed. The weed bends as he steps on it, and it is flat. It is a prop.
Continuity mistake: While Mulder climbs down the inside of the spaceship, when he enters the second hole he wears gloves but when he falls out of if the gloves are gone. (01:27:20)
Continuity mistake: When Mulder encounters the Well-Manicured Man, all doors of the limousine are closed. However, in the next shot the driver's door is open. (01:17:25)
Visible crew/equipment: Near the entrance of the building, when the fire brigade arrives, a guy holding a boom microphone is visible. (00:19:25)
Answer: Mulder has just hit rock bottom and is questioning just about everything at this point, so drinking is not really out of character.
Grumpy Scot