Couple of factors I can think of.
One: the first plot of Persona 5? Basically woven / ripped from news. Kamishiro is an exaggeration, but... an exaggeration that's based on things that happened. Haven't done a search for how many stories he's a combination of. (If you don't know the plot, short of it? Gym teacher who abuses students, and focuses on females. Not out-rite stated, but favors of a specific sort are demanded by him are implied.)
Two: They are incredibly regimented. To the point where there are tales of girls having to dye their hair to 'not distract boys' if it isn't the typical dark / black.
Three: Same as above. Supposedly to the point that some schools have what types of underwear are appropriate on their books. And again, tales of it being checked / enforced.
Four: Face saving. I know face is very important in Japanese culture, but I do recall several cases where nasty shit occurred, and got buried to save face. Shit eventually got exposed after more students were hurt (ties in to one, but it's systematic rather than bad actor/s).
- Yeah, I know, name an organization that doesn't do that, but still valid.
Five: Again regimentation. But this is more along the lines of the leaders of the system having data showing that it's actually hurting them but being determined to stick to the course if not double down. At least, I recall a documentary, article, and a few youtubers talking about it (don't ask for names, that was a few years ago).
And more generally? All the mangas and anime that show students doing things that are fairly wild? Odds are the writer / mangaka daydreamed of doing that while stuck in a monotone. The system seems to be good for STEM and those that want that, poor for the more artistic that want to march to the beat of their own drum. And if the writer is that sort of type, they'd see it as bad.
Ah, and six: could just be casual racism / 'we're better than you because I say so'. Can't count that out as being a reason.