The submarine force has had its share of mishaps, most recently a string of them in the 2010-2012 timeframe.
The biggest difference is the way in which submarines practice organizational control. The entire service has adopted the nuclear power model, which means that supervisors have heavy involvement and frequent monitoring of the operation of the ship. This is to keep standards high and to mitigate the risk that the article talks about - ensuring we keep the surface:dive ratio at 1:1. For example, the SWOs I know were surprised to hear that we tour the entire ship prior to relieving as OOD/SDO.
The qualification and proficiency process is also more stringent. I don't know how many QM3s or STG2s get qualified their senior watchstations by a surface CO, and I'm not sure how often he watches a GSM conduct a routine evolution, but it's probably a lot less than a submarine CO does.
The biggest surprise to me is that, according to Navy Times, the crews reported that they did not have time to train because they were underway too much. A submarine with a high optempo will very easily be 'green' in all those CTQS attributes.
I'm curious if the surface force has the same deployment preparation period cycle where the ISIC is certifying the ship at every step.