(at around 28 mins) When Scully enters the Assistant Director's office, the US flag behind his desk is hung upside down.
The sub captain talks on a voice-line via radio to his higher command while underwater at cruising depth and below a "32-foot" ice pack. Radio waves propagate poorly underwater, and this has always been a problem with sub communications. A sub needs to approach the surface and raise an antenna very close to the surface to exchange voice messages (although they can receive short messages on special low frequencies while deeper).
At the start we are shown USS Allegiance at a 'cruising' depth of 1000ft.
Modern military submarines have maximum dive depths of 820ft to 1300ft.
This submarine would not just cruise around near the limit of it's dive capability
because of the safety implications and that the stress weakens the hull over time.
(at around 1 min) Mulder starts chasing a guy through the submarine with his torch. He turns left to go down a corridor which is lit at the end of a hidden white light pointing downwards. When Mulder gets to this point, the light goes out, to leave just his torch as the lighting source.
Mulder meets Mr. X at the Kennedy Center in Washington, at night. Stock images of the building show it awash with downward-pointing white spotlights on all outside walls. In the establishing shot, all those lights appear to have been turned off. Later on, there appears to be limited up-lighting of the walls, which in real life have much more down-lighting.
At 4min 33sec Scully is thrown onto a glass table. The tabletop begins to break from the left hand side just before she impacts it.
The Captain of the submarine is shown with a beard. Beards have been unauthorized in the Navy since 1981.
There is no "91st Street" in Rockville, Maryland.
If Mr. X knows that Mulder has gone to Alaska, why go to his apartment in response to the X signal?
Edit: it is probable though that Mr. X wasn't aware of Mulder's excursion and only when he realized that his superior and his partner are both looking for him, he was able to make an educated guess that he shared with Skinner.
Edit: it is probable though that Mr. X wasn't aware of Mulder's excursion and only when he realized that his superior and his partner are both looking for him, he was able to make an educated guess that he shared with Skinner.
The submariners have their name tags and submarine warfare pins on the wrong sides of their uniforms, and the submarine warfare pins are at different heights on different uniforms (the Captain's has a space between the pin and the pocket, as it should, whereas LT Wilmer's badge is overlapping the top of the pocket).