It happens to me in every single game, but generally much quicker with packmule. It's a lot annoying. Especially because pill bottles and such split into different items once you use one of them, further exacerbating the issue if you use comestibles all the time like I do.
Actually, the thing that kills me most in this game is inventory management and encumbrance. And this is coming from someone who loved Incursion's system. Make it so containers actually hold items to help alleviate the max item limit, which would probably be an absolute total re-work of inventory and a giant pain in the ass at this point; or simply remove the silly item # limit and attribute letter assignments to items only while they're being shown on the screen.
I don't use hotkeys for items anyways, unless it's assigning 'a' to a crowbar, mostly because the keys always seem to change all the damn time for no reason, making me search through my inventory to find the item I had thought I memorized the key of. Keep the highlighting of selected items and just get rid of the assigning-letters-on-pickup bit. Make the items in the inventory itself of less import and only worry about weight/volume limits.
But yeah, basically the item limit is hugely immersion breaking and rather unacceptable in the game where packmuling and being a nomad is one of the most viable playstyles. I dunno, I just don't want to be forced to have a car or a dump building simply so I can continue to pick up pill bottles and nyquil.