Running Ver 1.9.3.66065 and these mods:
When I scrap something, the Scrap button of the independent items in my Store is disabled and I can no longer click it. Until I scroll, that is. As soon as you scroll the list, either with the mouse wheel or the scroll bars or whatever, the buttons are enabled again and you can actually scrap the independent items.
Here is a movie on how it happens:
My guess is that at some point there was an idea to not allow scrapping of such items and even after it got discarded, some code was left over.
Please fix.
I never had this issue, so probably you should try it without mods first and when it then also happens press F10 for the ingame report tool. This way the devs get your save and anything that is relevant to look into the problem.
Thanks for the F10 tip but a savegame is not needed here, they surely have some indy items laying around 
I just tried it without the mods, it still happens.
Even then, F10 is the way to go to report bugs because this way they get it directly 
Edit:
And also because it didn’t happen to everyone they can track this issue with your circumstances.