I'm having this same problem while testing - it doesn't matter what map or which mob I'm fighting. They aren't falling through the floor, they're just vanishing mid-combat.
So far it's happened to Borg NPCs, Breen, Devidians, and Fek'irhi. On the ground, it seems to occur more often when my weapon causes knockback. It is possible that the short time that knockback effects leave the NPC stuck may be enough for the AI to delete it.