I believe it has to do with how they hard coded the game. They didnt incorporate hiding on the bottom into it. At least thats how it is for us folks with SH3 Im not sure about 4 and 5 but Im pretty sure itd be the same thing.
If not my guess is he picked you up before hand on hydrophone (if you were making noise) or got lucky and guessed where your torps came from and just started making runs when he hadnt picked you up
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