Looking at the code, we use InventoryManager.retrieveItem to get a clover. That will pull from storage (if you are our of Ronin), buy from the mall (if you have the mall purchase option set) - and will remove from the closet, if you have the "use closet" checkbox selected.
If you do NOT have the "use closet" checkbox selected, it would be a bug were KoLmafia to remove things from there.
Therefore, it sounds like in part 1 of this "Bug", KoLmafia is behaving exactly correctly.
Part 2 - redefining "lucky" to mean "clover or nothing" vs. "clover if available" - is worth considering...