and the pilot's could not fly the aircraft properly manually and crash. Is that not pilot error also? Due to lack of handling skills?
No. That's a fault in the Training and Flight Operations departments of the organisation concerned. Pilots can only do what they have been trained to do and what they practice. If the SOPs forbid manual flying and it's not practiced in the sim you can't expect the pilots to perform. For example, I couldn't knit if my life depended on it.
When things go wrong it's vital to look at the system behind the operation. A classic example of this was the Kings Cross fire. Any public building should be able to tolerate a dropped, burning cigarette. London Underground did not anticipate that one cigarette could set fire to years of rubbish which had accumulated under the (wooden) escalators. The top level of the system did not identify the hazard. Nowadays, not only is smoking forbidden on the Underground but I bet the underneath of every escalator is also scrupulously clean.
PM