Is this a known issue/bug? I was doing the clover daily from Lara in Heidel and when I completed it, the item did not store itself with the clovers that were already in my inventory but instead made a duplicate of itself.

Pic for clarification.

Just withdraw them to inventory and put in storage again. Easy fix

Yeah this happen if you put the stackable item into a slot that then will be not avalible anymore (ie.: your VP runs out), and if you move the item from the locked slots, then it refuses to stack.

Soul's comment(puting both in storage and then withdrawing) fixes it, but still a bug.