Hee, I think the debate about whether or not Mulder actually mouthed something in DeadAlive (along with Scully doing the same in an upcoming ep - don't recall which one at the moment) was one of the biggest debates at the time. It's one of those things we never got a definitive answer on.
On the one hand, it's XF so who knows, they do what they want to. On the other hand, since by this time they are pushing that we are all descended from aliens in the first place, and are thus in part alien, it makes some sort of sense.