Yeah, the game definitely have an issue with items.
I believe it's due to elevation and in fact, elevation, in general, seems to be quiet a problem in this game.
If an item is located at an elevated position (on a table, for example) and I can't pick it up, usually climbing on the table allows me to interract with it.
Now, it's true that it happens quiet a lot with items that are on the ground too. Maybe they're considered too low to be picked up or the problem is something else entierly.
On the side note, enemies have a fairly hard time dealing with elevation too. I was able to run over them from an elevated position and they don't notice anything...Also, enemies tend to glitch through the floor if it's elevated so, yeah, elevation in general seem to be broken and are one of those things that needs fixing (I'm pretty sure CDPR acknowledged it already, I'm very confident that one will get fixed eventually).