If you mean the Fuji Excursion it's because the Kawaguchiko side isn't the same agency so it's not like JR has machines there. JR's intended solution is digital tickets but I think this doesn't quite work with JR Pass.

That was the one. I get the reasons sort of, but as a traveler it sure was strange that I could buy the one-way ticket, but could only retrieve it at the destination and so couldn't board. Anyways, we ended up taking a bus instead.