First off it shows you the three torpedoes in reserve and the one in the tube, that purple thing next to the torpedo count is the one in the tube. Its like the missile counter. To my knowledge there are only three targets you can lock onto with torpedoes and that is; Destroyer bridges, Destroyer shield generators, and space station main comm arrays. You are having an issue with the destroyer shield generators. Without unequiping the torpedoes the only ways for you to destroy them are to use your laser cannons or just use the torpedoes. You can do these missions WITHOUT using regular missiles on the generators, you just focus them once the ship is in range just pay less attention to the frigates and keep moving...also upgrade your ship if you need to.