This happens on two occasions i believe:
- first with LMG because you cannot drop mag boxes with an LMG. Therefore, if you reload a mag that is not empty it is being stored and can't be resupplied.
- second: might also happen with any other weapon when it has a full mag loaded including the extra bullet in the chamber (so you cannot reload & drop a mag). Not sure if stored half-empty mags will be resupplied but i guess they don't get switched either.
So basically this happens when you are carrying the max amount of magazines, no matter how many bullets they hold at that moment. Only completely empty mags are being dropped automatically and can be resupplied, as well as manually dropped mags (which is not possible with LMGs).
The ammo boxes need some kind of "resupply policy". Like for example they add or replace (used but not empty) three standard mags including extended mags, or two drum mags (standard weapons and LMGs), or one ammo box (LMG, 100/200 rounds) except the mag that is currently loaded. I think this would be the most feasible way.