Necrosia, it looks like there are only two possibilities.
1) As mentioned before, Torpedos act like missles in the interface. The loaded torpedo does not count towards your reserve total, and you have four. How you are only destroying three generators with four torpedos is puzzling, but there it is.
2) You are telling the truth, and you are only able to equip and fire three torpedos, leaving you unable to complete the mission. If this is the case, then this is a bug. Submit a detailed report, then avoid the mission until the bug is fixed.
Cheers.
To be fair, I have not attempted the mission myself, nor have I gotten the Torpedo launcher. However, even the tooltip on the torpedo launcher mentions it loads with four torpedos, so..