These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Pedro. The guy's an unrepentant rapist, has attempted to sexually assault Minoru three times, deludes himself into thinking that Minoru's being a Tsundere towards him, and later has the gall to assume that Nana, who has been Minoru's best friend for years and stuck with him through thick and thin, is a depraved stalker.
The only openly gay character for most of the series is a former rapist and makes sexual advances towards Minoru nearly every chance he gets, even when Minoru clearly isn't interested in him.
Virtually all of the foreign characters, from the American soldiers stationed in Okinawa, to Samart, to the above-mentioned Filipino gay male, have very unfavorable depictions.
There's also the first transgener character to appear, who is mainly treated as comic relief and whom suddenly stops being treated so nicely once the fact that she was born a he is revealed. The scene is depicted in a way that makes it seem like we should sympathize with the greater cast, who were "tricked" about her "true" gender, rather than the transgender woman who had her pants pulled down in front of a bunch of strangers.
Let's also not forget the double-standard depictions of sexual assault. When it's a woman being assaulted, it's treated with the utmost seriousness—and rightfully so. When a man is both the perpetrator and victim however, it's comedy.