The game can reload sunk ships, if it scripted to have that ship sail again. So if you happen to sink a specific ship (warship),and still are on patrol when that ship is scheduled to sail again, you might see it sail by. I think I got the Hood twice in one patrol once.
As to your original question, Weather and other game elements can impart damage onto ships. If the weather was bad, it could cause the last few hp's of damage to the nearly sinking ship, robbing you of the kill. Other times, other vessels or planes can get that last hit in, again stealing your kill.
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Luck is a residue of Design.
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