check if your Sovereign HP has its torpedo section of the ship HPs to look like this:
Torpedoes.SetMaxTorpedoes(0, 350)
Torpedoes.SetTorpedoScript(0, "Tactical.Projectiles.PhotonTorpedo")
Torpedoes.SetMaxTorpedoes(1, 0)
Torpedoes.SetTorpedoScript(1, "Tactical.Projectiles.QuantumTorpedo")
Torpedoes.SetMaxTorpedoes(2, 0)
Torpedoes.SetTorpedoScript(2, "Tactical.Projectiles.PhasedPlasma")
Torpedoes.SetNumAmmoTypes(3)
even if you don't want your ship to have Phased Plasma torps, there has to be an entry for it nevertheless)...
also, check the HP of Sovereign E3M2 to have the same 3 torp entires in scripts/ships/hardpoints folder
if that doesn't work, please provide a console report...
there is a stickied thread in Tech Support forum that explains how to go about obtaining one...