How and when you save games mid-patrol also determines whether this well-known stock SH3 bug rears its head. Saving too close to the "action" has the potential to create problems (and more than just no credit). Saving before the ship is actually recognised by SH3 as sunk definately means no credit for the kill.
Best bet is to save your patrol once just prior to docking. Then if you have the problem, reload the save and dock again. This tends to fix it.
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