You're not alone. I've had that happen in both SH3 and SH4. Got into position, thought I had the sweetest setup, fire and watch in frustration as the torpedoes managed to find all the "gaps", LOL.
The lesson learned was to work more on my targetting/TDC skills and the fact that a "spread" may only result in minor damage even if you hit anything due to lack of concentrated fire if you get my drift. I haven't made the same mistake since, I now tend to be more selective with targetting and avoid firing a "spread".
Someone will probably back me up on this but I'd recommend you target a specific ship, fire two or three torpedoes, target the next ship, fire two or three torpedoes, break contact to reload (if the destroyers let you!!) then re-engage later. More probability that you'll hit your intended target with enough torpedoes to sink it as opposed to just hitting a ship with one torpedo (which, unless in the right spot/depth rarely sinks a large merchant).