Did the Luft' finish her off? If not it could be poor weather - I know that can rob you of your credit for a kill.
Speaking of killing multiples of the same ship in one campaign; I wonder how complicated it would be to have an option in, say, SH3Commander (just as an example) where you select from a list which "one of a kind" ships you sink after each mission, and they are then removed from the roster so they can't appear again?
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