I cant say i have ever come across any issues with savegames myself but have heard many similar stories to your own, i frequently save submerged/near convoys/sinking ships and have never experienced any problems. I never usually save more than 2-3 times over a whole patrol though, i guess if youre saving often youre multiplying the chance of getting a corrupted save.
This must be down to some file corruption somewhere, try a full reinstall of the game and see if that helps would be my only advice + make sure you dont have any special characters in your savegame name that may be giving windows problems.
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