I just wanted to chime in. I have the same problem. I upgraded Dying Light gun two times, now I have 3 Dying Light's and I can't destroy, stash, or drop any of them. Here are some details that will hopefully help with debugging:
Before doing the shooting range quest, I levelled up my crafting to 18, and I tried upgrading my gun twice. But the original gun was not consumed. It just made copies. Each copy had a yellow exclamation point.
Then, I thought maybe if I finish the shooting range quest, the exclamation point would go away (I read somewhere on the internet that maybe that would work). Funnily enough, ONE of the gun's exclamation points did go away after that quest (I think). Anway, there are two guns with exclamation points, and one without....but I can't sell/destroy/drop any of them.
All three guns seem to be tied to each other. For example, if I equip the Dying Light, then all three show up as equipped in my inventory. However, when I go to the "Stash" screen in my apartment, only ONE gun shows up in my inventory. However, if I try to stash any of them, I will hear the stash noise, the screen will refresh as normal, but the gun remains in my inventory.
After one of the exclamation points went away, I tried "upgrading" another Dying Light. The upgrades now generate completely new guns, which I can sell/destroy/drop. BUT the original three guns remain green and un-upgraded.
Hope that helps. Luckily my 3 guns is only 12 lbs. Some other users have hundreds of pounds of items they can't unequip which obviously breaks the game.
I'm afraid to do any more upgrades of any weapons now....especially if they have a yellow exclamation point. I guess I'll have to make a save before every crafting session. I really think we should be allowed to destroy any item, even those with exclamation points...we should just have a warning prompt us to make sure that's what we want to do before we break down exclamation point items. Or at the very least, we should be told that that item is a quest item or something and can't be "upgraded" until it's no longer a quest item? Or at least, when it's upgraded, ensure that the original is properly consumed. Hopefully, the bug fix doesn't just fix the problem going forward, but allows those of us already with this problem to break down any bugged item (at least with a confirmation prompt). Thanks.