It doesn't affect the correct use of the mod, it's just a little confusing when trying to remember how many finite items are available. Here is a brief description. I hope it helps to fix it. ;)

EXAMPLE FOR MAGNETIC RIFLE:

1. The Build Item Menu in Armory shows name "Magnetic Rifle (Squad Upgrade)" but it really builds a unit and not a squad upgrade and it also shows the number of items "built" and not the real amount in possession (if you built 3 and lost 2 in a mission, then it shows "Magnetic Rifle (Squad Upgrade) 3" but really you correctly have only one available.

2. The Inventory Menu in Armory instead shows twice the same item with two different names and two different amounts: "Magnetic Rifle 1" showing the correct amount (not currently assigned to any soldier) and also "Magnetic Rifle (Squad Upgrade) 3" explained in the previous point.

3. The Black Market Sell Menu instead shows the correct names and amounts available to sell.

p.s.
Armory Plasma Grenades are immune to this bug