There are two possible reasons. One is that you made changes to your U-boat before going out on patrol in your first career patrol. This is a known game bug. When in a career, do not make any changes to your boat configuration before going out on your first patrol. After that you may make changes to your boat.
The second reason is if you sink ships in shallow water. You may not get credit for a ship that settles to the seafloor in shallow water. This sometimes happens when you raid an enemy harbour. The upper part of the ship sticks out of the water and though the keel is bottomed, the game may not recognize this as a sunken ship and give your credit.
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