Are they the two torpedos stored externally? If so, have a full compliment of men in the appropriate torpedo room (froward room for forward external torpedo, stern tropedo room for stern external torpedo). Then, on the weapons amnagement screen, click on the external torpedo and 'drag' it to an open internal slot. If you then put the mouse cursor over the torpedo, it should show you the time to move it inside. (Usually 40 min. to an hour). Also, be sure you are on the surface, not in silent run, and an officer is at the weapons officer station.
Good hunting!
