I think the two things that negatively surprised me the most about Japan when I moved there and started talking to people:

First are that the press has less freedom than you’d expect for a democracy. I learned this after becoming friends with a local member of the Communist party.

Second, that although the police on the street are incredibly kind and helpful, often going out of their way for people, if you do get arrested, the treatment of prisoners is pretty bad. They are very good at getting confessions, even out of innocent people.