Is there any other reason than BILC that the assassin puts his gun in the trunk of his car after shooting the sheriff's son? Wouldn't it be more handy in his jacket or next to the driver's seat?

When Mulder is hunting the assassin in the meat plant, he notices the gasoline tanks ready for the blaze. Why doesn't he move them, so there's no danger of them going up accidentaly during the shoot-out/ struggle which will follow?

Due to a lack of nits for this ep I'll point out that the old man with the red truck makes a re-appearance in Piper Maru as one of papa Scully's Navy colleagues. Since this type of thing is fairly common I'm a bit surprised that Phil didn't mention this in the Guide.

Although it's surmised that the Red Museum cult may have been used as a control group I don't really buy that a group like that could attract as many followers in such a rural area. Also, why were they dressed like that? The average Indian isn't vegan, they just don't eat beef.

Phil touches on this point but when Scully tells Mulder about what was in the empty vial found in the Dr's briefcase she claims it was purity, yet there was no proof that it was extra-terrestrial. Well, actually there was proof, which Scully was even told about, that evidence is just not presently available.