Have been unable to recreate so far. Does it happen often for you? Are you using hotloaded? If it happens again, maybe check if refreshing the inventory by pressing inventory button removes the item - it does seem that in some conditions the used up ammo isn't removed, but for me it retains the pre-reloading stack size, instead of 40.
Thinking about conditions which could give rise to problem (not all of them are, and it may be something else).
1) No ammo in personal or stash
2) Some, but not enough ammo for reload in home inventory
3) Some, but not enough ammo for reload in personal inventory
4) 2+3, but weapon still not reloaded