Tried it with all the other mods disabled, it still happens. Also noticed that the Black Monolith appears on the ground around shrines even when you don’t have any Black Monoliths picked up.

Black Monolith is also incompatible with RiskyMod

or atleast until you pick up a monolith item on the stage you're on. otherwise you cannot reuse shrines.

If you enter a new stage the monoliths cease to function.

Making it a consumable item like regen scrap would also be much better than what it is now.