I am currently getting monsters that are invisible and sometimes untargetable. they also hit really hard and have killed me numerous times. Graveyard and Beehive
Did your game patch correctly? Can you use the command Show Names (you can set an hotkey for that) to tell me the names of those invisible mobs?
Certain ranged mobs can shoot you through walls too, like at bandit camp inside the building.
Might be a floor issue. Monsters can target and try to attack through the floor. So don't put your rooster perches over your Melonite patches.
I experienced this in the beehive 2nd basement level. You can't kill them. I think it's a grub or one of the nymph bees.