Eh, if any particular crossover is extremely difficult to reconcile with other established facts in either of the shows, movies, comics, etc., you can probably brush it off with the old multiple universes theory. That is, you might see a character that is familiar to you, like John Munch showing up on The X-Files
, but that doesn't mean he's necessarily the same John Munch that you've seen from the universe of Homicide
and Law and Order
; he's a John Munch from an alternate universe, who just happens to also be a Baltimore cop.
Of course, that reasoning can be difficult if the crossover has important and lasting repercussions on both shows/films/whatever. I guess you just have to do the best you can.
Iím aware that the character Jose Chung appears in one episode in both series but does that even count as a crossover?
Sure, I don't see why not, especially since he was a memorable guest star in both. Add that to Frank Black's appearance in an X-Files
episode, and I think that pretty much states that the two shows are definitely set in the same universe.