Did you save game and reload between when you hit them and when they were reported as "destroyed" (and turn into a sunken ship icon on your map)? In SH3, when you loaded a saved game under those circumstances, when the ship did sink the game seemed to forget that you were responsible for damaging it.
I have only had one missing kill -- an aircraft that I saw go down (it nearly hit my sub) but there was never any "target destroyed" message and nothing was entered into my log. But it was just a stupid plane, I was just happy it didn't succeed in kamikaze-ing me.
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