This happens with crossover fics a lot, I've noticed. There are a lot of crossovers that sound interesting in theory, but once you try to actually write them then the differences between the two stories/worlds make it impossible. The characters in one world are more developed and it makes the characters from the other look thin or even incoherent. One of the stories functions on that slightly absurdist sitcom logic that doesn't fit with a more down-to-earth canon. Or the world-building is just incompatible.

I think this last one works against Harry Potter crossovers a lot. The worldbuilding has a distinctive weirdness to it that makes it hard to mesh with anything else.