Your damage control only repairs damage that is repairable at sea. All damage is cumulative, however. So all those little attacks weakened the hull. The result of such "hitpoint" damage is to raise the crush depth of the boat. Once the crush depth is the surfaced depth, that's all she wrote, you sink. In your case, the crush depth was just below the surface someplace.
The game shows you that something is wrong---inside the boat you will see leaks, etc, even though the boat is "repaired." That's a serious warning!
If you don't see those after taking damage that you worry might be bad (a near DC or bomb, for example), make a test dive---when you see leaks inside, go up til they go away, and try not to go that deep again.
tater
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