If I have two items in my inventory that have the same name, and I have one with better stats or mods, so I decide to discard the lesser worthy of the two. After I do this, the game destroys both items. It happens consistently. If I have multiple with the same name, it’ll destroy them all instead of just the one I have highlighted.
Video clip I took where I pick up a shield, and destroy one but then both get removed at the same time:
It seems related to the item name, it happens with every item. If you own multiple items with the same name (not category or type) by destroying one will destroy every copy.