When Mulder arrives at his former X-Files office at the FBI, he kicks at and tears the 'I Want To Believe' poster lying on the ground. However, in The Truth (2002) (end of the series' original unbroken run), Agent John Doggett rolled up the poster and took it with him.
Numerous previous episodes have shown that alien blood is toxic to humans, it causes severe burns on skin and is deadly when inhaled, which is why people working around alien blood had to wear protective gear and gas masks. However the Army doctor is shown picking up the alien's body, which is bleeding heavily from multiple gunshot wounds, and is not suffering any ill effect from contact with the alien blood.
During the flashback to the alien craft crash site, the alien is shown lying face down after being shot and when a paper cover is drawn over the body. But in the very next instance when the body is being lifted, it now appears facing up.
When Scully attempts to use the search engine, she receives "Error 404 - Site temporarily unavailable". Hypertext transfer protocol status 404 is a "Not found" error. An site unavailable error should generate a 503 status.
As Mulder steps out of the home of Sveta to greet Tad O'Malley, arriving in his helicopter, the camera crew can be seen in the reflection of his sunglasses on two occasions.
When Mulder exits the Uber driver's car in Downtown Washington, DC, a Canadian-spec "Do not enter" road sign is visible behind the car (red circle with white dash through it and no text). US-spec ones would say "DO NOT ENTER" above and below the white dash.