Martini-Henry's ammunition.

As you guessed, the matter of ammo resupply isn't really a bug, but more of a combination of two working mechanisms that, in that one case, produce a poor end result. 

So, first of all, each ammo box can only resupply a certain number of 'units' of equipment. One unit generally is: a single magazine/clip for the gun, a grenade or a single explosive. After resupplying a set number of units (7 or 8, I think), ammo box disappears.

Now, to the second part. In case of Martini-Henry, a single 'magazine' is one bullet. For that reason, the game registers resupplying 6 Martini-Henry bullets as 6 'units'... and that pretty much uses up the ammo box.

In the end, while neither of mechanisms is a bug alone, when combined, they kind of mess up the end result. Probably the best solution would've been treating more M-H bullets as one resupply unit, but I don't know if it's possible.

Regarding the second thing, it definitely is a bug, so good catch on that.