That often happens when there is also another mod for widescreen resolutions applied to the game. Then the mousecursor is released to the fire button location and accidentally fires the torpedo when clicking.
This thread covers the same issue:
http://www.subsim.com/radioroom/showthread.php?t=189092
Frau Kaleun has a link to disable the fire-button, forcing you to fire with only CTRL-Enter.
Or use a GUI mod that is made specifically for widescreen resolutions.