Well, I have a similar problem. I'm using TM1.7, maybe thats the reason.
So I stumbled upon this nice juice convoy, got into position to shoot and saved the game. Happily threw out 6 torpedos, then had to alt-tab when the torps were half there and because I had some crashes with alt-tabbing I saved again. Well then, 4 hits, two misses. Ok, I thought, lets try this once more. Loaded the first game and... um... the convoy was gone!

6 times "Torpedo in the water" although there was no torpedo in the water and a good bit later 6 times "Torpedo missed" without any explosions or anything. Then I loaded the second save with torps under way and there was nothing! No torps, no ships, nothing except my sub.
Funny thing is, the hydrophone contact markers are still on the map, but slowly fade away, because there is nothing there any longer.
Do others have this problem, too? Is it due to the patch or TM? Do you use any mods, propy?