So I have to look into this more. But i've noticed on several different occasions that if i pick up a new box of ammo or clip of ammo, put it in inventory, then go to empty the bullets out of it also into my inventory, if i had previous bullets of the same kind, sometimes the amount of those bullets will change to zero (so that i can not use them, but they are still there). Now, it is not just adding the bullets for me and combining them, it seems to actually be erasing ammo.
For ex:
I have a stack of 38 5.56mm ammo, and another stack of 30 5.56mm ammo. I pick up a 40 round clip containing 40 5.56mm bullets. I put that in my inventory, then i click empty on the clip, then the 40 5.56mm bullets will appear, but for some reason say the 38 5.56mm ammo will now have 0 bullets.