Seems a bit of a jump in imagination that a box of ammo or pile is totally ruined with one bullet. The answer would be to split all your piles of ammo as low as you have space for.
This is alpha and anybody that has played this game much will realise this is a mechanic in the 'alpha' state and not worth worrying about from a player perspective. An educated guess would give the assumption that the mechanic would eventually be a 'chance' to split the ammo into a useable state similar to the chance to get sick from rotten fruit atm.
Please do not put a draconian fix in place that will have to be replaced by a mechanic that is more intuitive and works better for gameplay.