I don't know if anyone's attempting a Mystara campaign with the Pathfinder rules in this day and age (or ever), but I thought I'd make a post here. A number of monsters in the Pathfinder Bestiary 6
could be adapted to Mystara; the various fey could fit in one or another of Mystara's faerie courts, the outer planar creatures could be stuck in one or another of Mystara's many outer planes, the various Lovecraftian creatures could be servitors of the Outer Beings, etc. But here's a quick list of things that seemed more specifically Mystaran (though I'm still pretty loose in my interpretation of what might fit).
CN fey who haunt dreams. Found in the Dimension of Nightmare?
A gargantuan aquatic worm. Similar to BECMI's sea leviathan.
Intelligent oozes created by ancient reptilian druids, which turned against their creators. Cave blights are radioactive. In Mystara they could be remnants of the Great Rain of Fire, and/or created by the carnifex.
Similar to BECMI's vampire roses (X2 Castle Amber).
Corrupted brownies, depicted with calves' heads.
These are plants, though they resemble undead. Similar to BECMI's dusanu, complete with spore attack.
Could be remnants of ancient Blackmoor, closer to the time of Uther than the high technology of its later centuries.
Hollow World, Isle of Dread.
: Corrupted sasquatches.
Unlike the BECMI creatures, this version is chaotic evil.
Similar to BECMI's grab grass (X2 Castle Amber) but also they feed on blood.
There's a BECMI creature by this name.
Great Old Ones:
Conceptually similar to the Outer Beings
that appear in some fan works.
Subterranean, albino humans. They're telepathic and they can read objects. Could be used as Cynidiceans?
Could be inhabitants of the Dimension of Nightmare.
Negative energy creatures with the power to command spheres of annihilation. Could be lords among the blackballs.
This utukku is very different from the utukku found in the Savage Coast Monstrous Compendium Appendix.
Wolf-headed humanoids (like BECMI's lupins) who can transform into wolves. They hate werewolves.
Corrupted psychopomps who personify various mortal fears. They live in the Ethereal Plane. These don't correspond to anything Mystaran, but they're tied to the psychopomps, who have a place in Mystara's Limbo, and Mystara has an Ethereal Plane, so...
Imagine a portable hole that slithers around, trying to eat you. Probably found in the slummier parts of Glantri City, an unintended consequence of the magical experiments performed by the wizards there.