- Crowning Moment of Awesome/Crowning Moment of Funny: David Duchovny's uncredited cameo in the season finale, and the ensuing conversation between Mulder and Jimmy.
- The moment in the dance contest episode where Frohike bails out on the guys and isn't seen until near the end - turns out the short, homely fellow was once "El Lobo," the tango champion of Miami and had to go find his old dance partner.
- Fanon Discontinuity: "Jump the Shark" was not well-received, and at least a small portion of the fanbase claims Fletcher was lying through his teeth when it came to the Gunmen's fates.
- Word of God confirms that Fletcher did just that and the Gunmen are alive and well.
- The IDW comic, meant to be a canon continuation of the show, further confirms this. Heck, they got to star in a major event crossover!
- "Funny Aneurysm" Moment (Just watch the pilot.)
- Harsher in Hindsight: The pilot episode, which aired March 4th, 2001.
Byers Sr: The Cold War's over, John. But with no clear enemy to stockpile against, the arms market's flat. But bring down a fully loaded 727 into the middle of New York City and you'll find a dozen tinpot dictators all over the world just clamoring to take responsibility, and begging to be smart-bombed.
- Then fast forward six months later to September 11th...
- Narm / Special Effects Failure: Tom Braidwood (Frohike) and Bruce Harwood (Byers) are standing on a fully visible Scully Box in the promotional shot used for the cover of the special edition comic book. It... somewhat detracts from the dramatic dignity of the shot. Seeing as the Gunmen were comic relief, this may have been deliberate.