Jorge had been hiding in the hut's bathroom since before Mulder arrived. But when Mulder got there, he had to use bolt cutters to break the chain that locked the hut's door from the outside. Jorge couldn't have gotten in before Mulder.
In Pilot (1993), Mulder reveals that his sister "disappeared out of her bed one night... no note, no phone calls, no evidence of anything, that, thanks to hypnosis, he recalls "a bright white light and a presence in the room," and that he was "paralyzed, unable to respond to his sister's calls for help." However, according to the flashback, Samantha was in the living room with Fox, not in her bedroom.
Mulder is in the receiver room, sitting in the chair and swigging
water from a bottle. He puts the bottle down on the table using his right hand, grabs a flashlight with his right hand, and gets up out of the chair with the bottle in his left hand.
When Mulder attempts to fire his gun at the figure standing in the light of the doorway at the Arecibo facility he pulls the trigger repeatedly as it fails to fire and a click is heard each time. Because it's a semi-automatic and not a revolver, a click would only be heard once during a misfire.
Mulder tells Jorge not to go outside the hut because there is a storm
outside. Leading up to this point, the background sound has been that of a seashore, not wind. Arecibo observatory is miles away from any seashore.
Mulder notes to his tape recorder that the main lights don't work in the receiver room, but that the instrument lights are still working. After he finds Jorge, the ceiling lights seem to work thereafter. This is especially visible when Moulder records that state of Jorge's body to his tape machine.
Young Fox Mulder is seen wearing a (Bernard) King T-shirt (right down to the correct jersey number, 30) from the New York Knicks basketball team during his sister Samantha's abduction. This occurred in 1973, but King was a freshman at University of Tennessee then; he wasn't drafted by the NBA until 1977 and didn't play for the Knicks until 1982.
Samantha calls Fox a "buttmunch." The scene took place in 1973, and the term "buttmunch" wasn't coined by Beavis and Butt-Head (1993) until the 1990s.
While Mulder and Scully are escaping Arecibo, the landscape seen is an alpine evergreen forest. There are no alpine evergreen forests in Puerto Rico.
When the soldiers are approaching at the end, Scully says "We're never gonna be able to get the body out of the country." Puerto Rico is a US Territory and therefore not a country.