If they couldn't be bothered to read the manuals then what can one say.
Software programs overriding manual control is nothing unusual, it ends up saving lives more often than not - humans are humans after all.
Someone who thinks that a pilots manual covers all the tiny technical details needs to read one. They can't possibly be large enough to cover everything, and they don't. A pilot needs to be able to find information reasonably quickly. That was definitely a abnormal thing for a pilot to do, but it should not have resulted in a accident. I'll bet the software was revised quietly later on. The FAA and EASA don't like computer software to promote accidents.
The OP mentions that this was a new plane and the crew was testing it without reading the run-up manual. Reading the manuals and the safety procedure is something the crew should have done. Probably the crew thought they had all the experience in the world to fly the aircraft and got too cocky.
Mishaps due to software have happened but mostly due to the fact that the crew were not aware of what the software would do in certain situations. Training should have taken care of such instances but this is where airlines have probably cut corners.
That said, there was no software error in this case ... it was the violation of test procedures that led to the crash - http://www.flightglobal.com/news/articles/violation-of-test-procedures-led-to-toulouse-a340-600-319969/