It's not common, but it's a notable widely publicized issue - so if you're writing a video game and you want a low-level antagonist for the hero to fight, it'd be one of the default options.

It’s common enough that there are women-only cars on the subway in Tokyo.

the problem is that complaining and making a fuss about things that bother you is frowned upon. especially for women. so they suffer in silence. and the games probably are mostly made by men, who of course don't think it is as much of a big deal. not much different from what it used to be in the west. if only samurai chivalry was more prevalent. but unfortunately keeping appearance (and not embarrassing others) is more important.