Regarding your first point (of murder and high treason
), you get a huge renow penalty after you complete your patrol (return to port). IIRC the penalty for a friendly ship sunk is 5000. But i think you will only see it in the patrol summary after you return.
As for the "torpedo missed" issue, i must say i have no idea. Sometimes i have notice the crew saying out of place things, "ship spotted" when there is not a soul in sight. but it only happens when i just reloaded a save.
Are you using any mods?