How many times have you been in the SIM and seen someone, when given a simple problem, get themselves into an awful mess through a lack of system knowledge?
Generally if people get into trouble for systems knowledge or lack thereof, it's from failure to follow procedure. When people begin trying to out-think the airplane rather than pick up a checklist and work through a problem, they get in trouble.
I do see people get into trouble by trying to follow through with the automation when they really ought to get rid of it. I had a sim partner once that could fly the airplane very well, but who insisted on doing everything on the autopilot. I understood that he wanted to learn that panel and work it well, and I understood that he'd been counseled to let the autopilot work for him as much as possible in the upcoming checkride. The problem was that whenever he started to get behind things, trying to fix it through the autopilot only made it worse. It might be that the descent wheel didn't start him down as fast as he'd have liked on the approach, and ended up high. Trying to catch up by increasing the rate would see him missing his MDA. Perhaps it was being a little fast or a shirt turn onto the localizer, and then blowing through the approach. In each case, he saw the problem coming, and disconnecting the autopilot would have fixed the problem for him by allowing him to handfly and correct the problem. Sometimes trying to work through something with the autopilot is a little like trying to run a race on stilts. It's easier sometimes, and sometimes more effective, to remove the stilts, shut off that autopilot, and fly.