Hi, at some places there are loot boxes and crates bugged in other items.
1. Angeras Church
One example here, i will post more in the comments once i find again 
I have TWO ammo boxes in that exact location/situation. One, as you see, that has a corner sticking out of the Plundra…and another completely inside the Plundra. The one with the corner sticking out is lootable, but the one completely inside the Plundra is not lootable—and only barely detectable.
There are indeed a number of other places like this, where loot containers or loose loot items are underneath other objects, or underneath the ground itself…
