Combat damage is the more proveable cause. There is no proof of how it sank, other than the hole in the forward near porthole, tested to be easily shattered by a rifled musket- a very lucky shot in the dark if it was indeed the cause of the hole.
There are possible reasons for the loss of the sub, but not due to the design.
1. Hypothermia (the crew exposed to water temperatures of the season, a crew already wet from sweat, and inactive, waiting for the current)
2. Anchoring the sub with the conning tower open, causing the current to pull the bow under and filling the sub with water. (a cause that actually nearly quickly sank a small modern sub.)
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David Upton