This goes for containers that can hold loot while also being in your inventory such as medical bags or protective cases. Sometimes when you have one of these in your inventory and they aren't full, when you pick something off the ground it will randomly be placed inside the container. I try to keep perishable items in these types of containers but sometimes I'll pick up loot, have no idea where it went, then a few minutes later realize it ended up in a protective case or medical bag. Not too big of an issue but it can be annoying at times.

Another related "issue" is that if you have one of these containers in your hand and there is an item in your vicinity, when you hit B to exit the inventory menu, it will put the item on the ground inside the container that's in your hands. The game must think you are trying to "combine" the item with the container. I don't believe this is how it's supposed to work but if it is then no worries.