Well, the 3 minute 15 second plot is good for getting a quick fix on his speed. But it isn't that accurate. It's better to take an average over a few intervals. 4 intervals are 13 minutes. Which is just long enough what the stopwatch can show. 12 minutes on the small handle, and another lap of the big one. And you get the speed known to a quarter of a knot. Much better the TDC won't take anyway.
But if the target really was at 500 meters in front of you then it should have hit anyway. 1 knot of speed difference alone cannot make that much of a miss at this distance.
The target can speed up if it does see the bubble wake of the type 1 torpedo. So it may have tried to dodge it successfully. Remember the near Tramp Steamer in the torpedo academy mission? How sure were you of your stealth?
Other than that I can only imagine the Torpedo speed setting bug messing up the TDC when switching between tubes with a type 1 and type 2 with different speed settings. In the future you can check this manually if it is correct with a rule of thumb (assuming near 90 AOB):
Lead angle= 60 * Target speed / Torpedo speed
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