Scully is usually right most of the time. Really there are only a handful of episodes where the spooky option ends up being the most plausible one. Even the stuff about Mulder’s sister and the “walk-ins,” which is ostensibly the most direct confirmation of anything supernatural in the show, is arguably an unreliable narrator trope since it is told to us by the show’s on again off again villain and “confirmed” by Mulder’s vision. Personally I don’t even consider that episode canon because it was such a thematic departure.