I recently noticed that when throwing or pulling things out of containers (for example chests, cork barrels) with the LShift key pressed, sometimes some of them disappear. I lost in this way valuable items such as: 6 golden nuggets, 15 oincs and 6 manures. This is really frustrating and I don't know what to do. I have several mods installed (among others Quick Drop) and they always works fine (I never had a problem with them). I think this bug appears when the game is playing in the background for too long. + I also have other bug with strange icons on the map (for example mushtree on the surface in hamlet) - someone already reported this bug many months ago.
Just play the game long enough, minimize the game, do something else on computer (browse or smth), return to game, play as usual, notice that some items starting dissapear when using contatiners.