@alm10965 I suspect it's mostly self-imposed discipline and, secondarily, peer pressure.
Like many Japanese workers, JR employees take great pride in precision and excellence. Any mistake, particularly those causing visible service disruption, make them look bad in front of everyone. A spontaneous and genuine apology would be expected.
@alm10965 With this level of self-, consciousness, there's no need for the boss to do anything to make a Japanese employee feel humiliated.
If an employee goes like "it's not my fault" or "come on, no big deal", *that* would seriously put their career in danger. Nobody likes a coworker who won't properly take responsibility and apologize. They'd be labeled as "selfish", and punished with silence or something.