Too much manual flying in congested air traffic environment can create its own problems.
People keep saying stuff like this, but really I don't see why manual flying would be particularly problematic. Looking at the ASRs at my place, it seems most screwups in busy ATC environments where because intended autopilot mode changes were not properly monitored and automatic mode changes were not noticed.
I would conclude that autopilot flying requires forced concentration and discipline, whereas manual flying imbibes such qualities. Therefore autopilot flying just a skill as manual flying is just a skill. Do enough manual flying and one wonders what all the fuss is about.