I’m having a hard time understanding why pilot error technically can’t be criminal negligence all the time? So I’m curious to find out some examples of this exact scenario, and how investigators determine if ones negligence is punishable by law.
Most countries will not prosecute pilots for accidents with good reason - the safety system depends on people being open and honest about their actions, so as to ensure someone else does not repeat them. Investigation agencies like the NTSB make it clear that their reports are not intended to assign blame, and so typically cannot be used in court for that purpose.
Pilot convictions for airliner crashes are quite rare but I can think of 2:
Garuda flight 200, where the captain landed 100kts too fast ignoring dozens of warnings, killing 21
Air France 296, where the captain on a display flight flew much too low and too slow, killing 3. France is a slightly different situation however, as every fatal accident automatically triggers a criminal (technically 'judicial') investigation alongside the safety investigation by the BEA.
Tuninter 1153, where after fuel exhaustion the pilot judged that he did not have glide distance to make an airport and ditched in the Mediterranean resulting in 16 fatalities. The captain was convicted in an Italian court of manslaughter and was sentenced to 10 years. The first officer and the chief operating officer of the airline also received prison sentences.
There are some more examples from the General Aviation world (light aircraft), where you don't necessarily have the same professionalism and certainly not the same oversight and standards from an airline, but the principle of refraining from criminal proceedings remains the same.
In the US, negligence would imply willfulness. Errors and accidents don’t imply willfulness nor negligence. That’s the difference between a death caused by an automobile traffic accident due to weather and one caused by a drunk driver. The latter is criminally punishable. The willfulness to do something wrong or not do something right is negligence. Making a decision that an average person would consider reasonable should not be prosecuted. Even if it is the wrong one.
The converse of making a reasonable decision in the case of flying would be to willingly fly the aircraft in a manner beyond the pilots capability or legal competency. If the pilot is not certificated and current, or flying the aircraft into a situation for which it is not certificated could be considered as negligent. The pilot had to do so due to an emergency, that would be a different story.
The same is true regarding intent. If your intent was to break a law, rule, or regulation (even if you did not know there was a law, rule, or regulation regarding your actions), that is criminal. A prosecutor or FAA official can even argue for the criminality of breaking a recommendation, best practice, or commonly accepted procedure if your actions led to an accident, injury, or fatality.