>it's a crashing this plane with no survivors episode
>It's a scully refuses to believe in the paranormal despite witnessing it firsthand countless times episode
Seeing it from the outside and knowing aliens exist basically gives up hindsight in the present, for Scully seeing isn't believing because it's not a rigorous enough proof. She purposely keeps Mulder grounded and constantly verifies everything so they don't get lost with their head in the clouds.
Even though I say this if you watch X-Files from start to end she does actually start believing at some point not too far through the show.
She's not stubborn she's reasonable and rational and cynical like a good scientist, it's not something you expect in a sci-fi which is why I think it confuses people.