Is this a common situation to find oneself in?
Does someone explain the rules or do you just figure it out by what every else does?
Does no one complain or quit in frustration?
Does anyone try to stop this practice?
People get explained the rules in the same fashion that Americans learn that work starts at nine, being late is discouraged, and that accepting bribes is improper -- yeah, if you slip up, you'll be reminded of them, but they're for the most part cultural background. Do you remember the first time you found out that your dad had to go to the office every day? Imagine finding out, that day, that he was going to be there until 11 PM. And that's just how it was, for nearly everybody you knew. And if it wasn't the case for your friend's dad, you'd keep quiet about it, because you didn't want to embarrass your friend that his dad had a crap job. That's the kicker: these jobs are the brass rings that people aspire to. (And if you wonder why I go on the warpath when folks suggest the Valley-esque work/life balance is to be emulated, there is why.)
More than quitting in frustration, the bigger phenomenon is younger folks just dropping out of the traditional labor force, which is a large (though probably exaggerated because it is shocking) phenomenon in Japan today.
The government and industry have made a lot of noise about humanizing working conditions for the last generation. We get reminders to stretch now! Yay! Seriously though, the cult of salarymanhood is very gradually losing cultural hegemony, partially because some companies are abandoning the lifetime employment guarantee (without which it is a very, very raw deal), partially because the Japanese labor force is broadening away from Men Doing Men's Work Like Manly Men which was always the core of the system, and partially because all cultures change over time.