Hmm Edit: Apologies, forgot to put thoughts into words.
I've seen backpacks fall on the same tile as enemy's bodies. Now realizing may sometimes lead to clipping issues. As you said such things are to be expected, I haven't reported them (apologies if should). There were bigger fish to fish. Other is when a part of body falls inside a building or other structure.
Is dropping given by map structure, can we influence it, or is it random? In other words, what do you mean by "Some of the items don't drop".
A few side-notes:
1. In case we can't influence this, I must say that would undermine tactical possibilities. Also you've put effort into graphical representation of weapons and this looting system. When seeing something I want, by a smart play can get and use it within the same mission. When the game says - too bad, see post-mission looting -> I won't bother anymore.
2. But the most important are allies. I often don't get a backpack for when they are KOed. If you don't want to encourage save-scumming I would say this is a fairly important. When they go down, it can significantly up the difficulty, letting us loot them would help survivors to survive.
3. I think I've seen an enemy eliminated early, with a pistol but no ammo in the backpack but his friends were reloading like 2-3x later on. Perhaps they get uneven distribution. But I may be mistaken.
4. That said, regardless if during or after mission, we are looting a lot of items. I guess this is part of the WYSIWYG approach. But maybe still something can be done about this - for example, via balancing durability & rate of deterioration, and money for an item depending on its state...