The best way to remove copies of cards is to use the grouping options. Select None to display cards individually and then remove each specific copy.
The best way to increase the quantity of a card in your collection is to scan it again or add it manually.
We used to have buttons to increase and decrease quantity but it was removed as it got confusing when deciding which specific copy to add/remove (particularly when cards have different tags).
We are considering new designs and will add it back in when we find a better system. Let us know if you want this functionality added back in as it bumps it up our priority list!