When the first two torpedoes are fired, their speed as shown on the display shows that they would hit in about 10 seconds, yet it takes nearly 40 seconds for the strike.
After the torpedo strikes near the front of the submarine, the port torpedo tube is exposed, with the forward (outer) door blown away. It would therefore be impossible for crew members in the torpedo room to load a torpedo into that tube, as water would flood in as soon as they opened the inner door.
After the minisub had rammed into the Inferno, a shot of the stern of the Manta clearly shows the minisub still attached to the Manta's hull.