i believe the problem is that ammo which is swapped doesn't go back into the crate like weapons do, it's just dropped. peculiar to flashpoint i think, not something you can change...
note - i
believe this to be the case, as i've witnessed it in my own missions; and as far as available 'space' in ammo crates goes, i don't think they can be maxed out.... i have my 'fireworks boxes' stuffed with 99 of everything, but it could as easily be 1000.
someone correct me if i'm wrong