mushrooms I can't get rid of

I have 2 of the the 3 mushrooms from the Apex of Filth area. I already completed it once (with all 3 mushrooms) and then picked up 2 of the 3 mushrooms again. I did a full clear trying to find the 3rd but did not get it. I'm not sure how to remove these two mushrooms from my inventory and it is annoying.