Maybe if we went back to the old ways, were the aeroplane was not trusted to do what you commanded it to & the PNF was not trusted to do what you asked, there would be less problems. Don't trust anything or anybody, not even yourself.
The PNF, when selecting the flaps should have checked that, 1. they were running after being selected & 2. they reached & stayed at the position selected. In the old days there were standard calls reflecting this. The PF should have checked that the flaps reached the position he called for. The same goes for any other selection that is made on the flight deck - landing gear, anti-ice switches, etc.
Takes a few seconds of concentration & discipline, but saves a world of heartache at the times things go wrong & don't behave as expected. It takes more than just understanding the equipment & how it works, although that is very important. It takes a healthy suspicion of the equipment & a constant cross-check that the aircraft is giving you what you have asked it for. That's what we have TMA's & FMA's for.
The excellent reliability of modern aircraft is one of aviation's greatest risk factors.