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.
Deoxys crosses this when he destroys an entire city, personally striking down the Pichu Brothers.
Ford has his partner Blaziken brutally torture Charizard, and turns Ash into Alpha Ranger.
Mariah nearly destroys May's psyche during their battle with her insults.
Dark Latios torments his sister, kills their father Ho-oh, kills Lady Ho-oh by ripping out her spine and eating her body, force-feeds Latias her father's genitals(!), and then repeatedly rapes her both physically and mentally until she becomes an emotionless killing machine.
Strangled by the Red String: Latias and the Ghost King's relationship is the most complained about aspect of the story. From the very beginning of the story, Latias has been dreaming about marrying the Ghost King, even though she didn't know what he even looked like. Later on, she forgives the him for razing her hometown and murdering everyone in it in a childish fit of rage, because two out of the hundreds of thousands of innocent dead said they forgive him. And then Latias marries the damn guy! Many readers were not at all satisfied with the story's explanation and especially not the tacked-on revelation that Kyogre secretly made the Ghost King do it at the very end, and consider this a Wall Banger.
So you want to try to apologize to your crush for destroying her city, killing all her friends, and ultimately traumatizing her. You can't go anywhere, so you need someone to convince her to come to you. So you send out your most loyal servant...who is also the one who killed your crush's best friend right before her own eyes. Oh, and he's also a Jerkass, and would rather terrorize her for several days instead of just bringing her right to you.
Fearow's gimmick is that he eats other Pokemon and gets stronger from it. So what happens when his minions capture Latias? Does he immediately grab some bread and have a dragon-on-rye sandwich? Nope, he tries to rape her for no reason, which delays him long enough for Pidgeot to rescue her.