I started noticing that my ammo stacks quantities would suddenly become 0.
At first I noticed this with the ammo that I was consolidating in my large capacity 5.56 magazines, but I started to notice this with my shotgun ammo, 357 ammo, .45 ammo, 7.62x39 and 7.62x51 ammo.
I believe it has to do with "emptying" a box, magazine, or other container holding ammo into your inventory where other ammunition is loose.
I thought that maybe the changed quantity was just a display error, so I tried to "combine" the now 0 stack with another stack, or load a weapon with the 0 stack to see if the quantity would snap back to its previous state.
No dice.