Honestly, I think the biggest problem with crossovers is that different canons have different base competency levels, and (unless the point of the fic is “I just want to drop [Character from Fandom A] into here so they can fix everything wrong with [Fandom B canon]”), the two canons just end up clashing.
It’s not even differences in tone, or the close-enough-the-differences-don’t-work worldbuilding (it’s much easier to, say, drop an angel into a world with no angel-canon, because you don’t have like - mutually incompatible backstories and ideas of hell or how it works). Discworld, for example, is a comedy, but it’s got a very high level of competence. Merging it with, say, Game of Thrones (much, much lower base level of comptence) is definitely possible, but takes a lot more work than merging it with, oh, Leverage or Prodigal Son or GBBO - where, just as with Discworld, a lot of people generarally know what they’re doing, and can (when push comes to shove), do it well.