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Some will clash gameplay wise, since Pixelmon is not built for Vanilla combat and by default deactivates mob spawns though. Additionally, mods that add dimensions or biomes may need some config editing to get spawns in those (Biomes O' Plenty, Traverse and Realworld are supported by default). Same goes for drops, if a mod locks resources behind mob kills and you don't want to activate mob spawning. Pixelmon is highly customizable for that purpose though, and we'd be happy to help with that if you need it.
We do have a page of incompatibilities that players encountered over the years on our wiki. But this list is not comprehensive and only updated sporadically, so we can't guarantee all entries are still correct - plus some of the listed issues may be rather minor or exceedingly rare: wiki/Incompatibilities_list
JourneyMap is also vital, of course, especially with icon mob display!