I am not sure as the surfaced condition but make sure you deselect silent running.
Silent running mode will prevent the torpedoes from being reloaded. So secure from silent running. Double check if you are not sure. Also make sure you man the rooms completely. Battles stations will increase the speed of reloading because everyone will be working in the room. Caution when crisis is over make sure to secure from battle stations as this will wear out the crew and stop them from sleeping too.
BTW
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