I've had this problem... I attacked a convoy, sank 2 ships. I saved and ended the game in the normal way.
Like a fool, I began playing with my mod soup while still on patrol.
I load up and play the game. Two ships come by, I sink them and they never register.
Turns out they were the same ship type I sank in the convoy earlier!
Do not play with your mods while out on patrol. It will mess up your gameplay.
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