[UKönig]

Yes, try not to ever save and quit after damaging a ship.
(conditions apply)
I'll try to explain as something very similar has happened to me on occasion.

If I hit a few ships in convoy and some are straggling it can take more time than I have to finish them off. So I save and quit and try later. Resume game. If a ship I hit previously sinks suddenly, with no more action or intent by me, then the game "forgets" who did the first damage, and it will sink with no trace, and even though I expended ammo, I will get no credit. No marker on the map to indicate sinking spot, no notice from the watch or hydrophones
There are variations of this bug, I think is made worse with bad visibility. So if you save and quit and resume later, try to get in another shot right away. the longer it goes with no more intervention by you, the less likely you are to get the points for your "work".
This is just something I have noticed after almost 3 years of almost exclusively playing SH3...