Not sure -- I always click "Refit" at Midway on my way to the Home Islands from Pearl Harbor, and I haven't had any uncredited sinkings after that. However, the difference is that it's only a fuel stop; I'm not taking on torpoedoes.
But I think it's more likely something else. In SH3, you sometimes didn't get credit for a sinking if you made it in bad weather and couldn't "see" the target from the sub (even if you used free cam to watch it go down). Could be something similar going on here, but that's just a guess.
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Jack's happy days will soon be gone,
To return again, oh never!
For they've raised his pay five cents a day,
But they've stopped his grog forever.
For tonight we'll merry, merry be,
For tonight we'll merry, merry be,
For tonight we'll merry, merry be,
But tomorrow we'll be sober.
- "Farewell to Grog"
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