Terrible instructions on the ammo boxes by the way. (For those unaware you don't encounter these until way late in the game)
Game tells you to touch them but not shoot bombs at them to collect. *WRONG!* Mousing over does nothing. I discovered you can use laser item and hit them to collect that way but it can only be done once in a level so it's not too feasible.
The correct way is to left click the ammo boxes but *NOT* release left mouse button. So you want to trigger a mousedown event but *NOT* a mouseup event if you want the ammo.