If it's my PhasedTorpedoes script (the one in FoundationTechnologies), then there shouldn't really be any lag.
What it does is get triggered by the torpedo hit event, calculate the new position (a small amount along the impact vector) and a new torpedo, exactly the same as the one that impacted, is created.
The only reason I can think of this happening is that either the ship is small, or it is moving fast.
In this case, it is probably the last reason that is causing problems here.
Changing the "duplicate" is as easy as changing the torpedo that you are firing (or another script that is firing a child torpedo).