Items re-appear after being removed by procedure

I'm making a mod for XP storage, basically when I use the remove item from main hand block, or remove item from inventory block, the item will temporarily disappear. If I go to a crafting table and craft any item (only 3) from my mod they will re-appear. When I use the lapis bottle for example, the bottle removes itself & gives the player an enchanted bottle (which stores the XP and removes it from player). For some reason when I use the enchanted bottle, it removes itself and gives back the XP, replacing itself with a third used bottle. If i craft the used bottle back into a lapis bottle the enchanted bottle re-appears, takes my xp back, and still gives me the new crafted bottle. No matter how I try to remove them, they always come back when any mod item is crafted.     Pictures of the only code in the mod (not much) > https://imgur.com/gallery/eKBZmDg