If I remember correctly there were two reasons why some boats were not having a full external torpedo load
1. The allied air cover was devastating so the boats had little chances to actually move the external torpedoes inside the boat.
2. At some point (later than the first attack in US waters though) it was discovered that depth charges cracked open the containers on the deck of the U-Boat. That meant that the boat was vulnerable (lower "Hull Integrity basically") and the torpedoes were damaged.
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