Maybe it is just luck, like the flipping of a coin. There have been obviously avoidable incidents in the past, where you wonder how anyone could be so stupid. I remember submarines crashing mysteriously or surfacing under a fishing boat in the last decade or so.
When the sextant arrived I am sure that there were accidents and people wondering if sailors had lost their skills, overly reliant on tech.
The Japanese tuna boat incident was a mistake that could have been avoided, but at least precautions were taken, as sloppy as they were. They were doing an emergency surfacing exercise and did surface to check for ships before doing it.
The chance of randomly hitting a tiny boat when surfacing are astonishingly slim. It was a bunch of factors, but mostly bad luck. I doubt a captain could hit a boat like that on purpose of they tried, there's just too many variables.
As a surface ship ramming into a boat is entirely avoidable. Those things aren't invisible, and those destroyers have ridiculous amounts of sensor equipment, active and passive.
When the sextant arrived I am sure that there were accidents and people wondering if sailors had lost their skills, overly reliant on tech.