Loot clearly clips through the ground occasionally. It seemed like it was happening less in 1.2 but now in 1.22 it seems to be common, again. Maybe I just didn't notice as much for awhile.
I spent a few months just not playing the game, so I don't have that comparison to make, myself.
That said, the most egregious examples are Samurai albums lying on the ground.
You can see them, they're clearly flush with the surface, the icon pops up, but the prompt to take them never appears.
I did
once manage to pick one up in the most counter-intuitive way (which only works about 10% of the time), by not pointing the reticle at it, instead looking up, horizontally, like normal, and walking over it while mashing 'F'. That works veeeeerrrrry occasionally.