The Loot Screen "Use" Button bypasses perk restrictions. I suggest removing the button entirely (to fix this issue as well as other issues w/ it) as Players can still use the Strategic Screen or the Equipment Screen to consume/use a Consumable Item and those two are working correctly.
Say you have a Champion/Sovereign with Merchant I and you get a new Scroll of Fortune. If you look at your inventory (Equipment Screen) and try to use it, this is what you will see ("Unit already has this perk"):
However, when you loot the item, you will see this:
On the above Screenshot, you can see that Serrane already has Merchant I (Yellow Icon). You can also see the Scroll of Fortune in the Inventory (First Icon above Level 2). Merchant I should prevent Serrane from being able to use the Scroll of Fortune (and it does if you try to use the Consumable from the Equipment Screen, see 1st Screenshot), but it does not prevent using the Scroll of Fortune from the Loot Screen.
If you do click "Use", you will get nothing as you already have the Merchant I perk. You will also lose your Scroll of Fortune:
(The Scroll of Fortune is no where to be found in the Inventory and Serrane obviously only has one Merchant1 perk)
LH Mods by Primal