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You must be surfaced - that's the most important thing.
Second - you can't drag them by your mouse directly to the torpedo tube, first you move them to internal storage (drag and drop) and then they can be moved to the tube. The first takes about an hour, the second about 10 minutes.
Third - be sure there is enough crew in proper torpedo compartment. Without crew nothing will happen.
PS And as stated above you cannot be silent running.