Corrupt savegames are an unfortunate fact of life with SH3, it's a known issue from the stock game. As Vendor has indicated, saving close to land or within contact range of other units is not recommended as it seems to increase the possibility of a corrupted save and/or CTD on loading. Saving when submerged can also cause problems.
The general consensus seems to be that you are safest when you save only while surfaced, and only when you are not within contact range (visual or via hydrophones) of land or any other units. It's not guaranteed to prevent the occasional corrupted save, but it will make it less likely to happen.
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