Just because an anime character looks like a nice person doesn't mean that they are. In fact, innocent looking anime villains crop up in series of all genres.
Sometimes, these characters look kind and helpful before their true devious natures are revealed, lulling the viewer and the other characters into a false sense of security. This is true of Malty S Melromarc from Rising of the Shield Hero, who tricked the protagonist into believing she was on his side so that she could frame him for assault. Some villains stay adorable the whole time, as is the case with Kyuubey of Puella Magi Madoka Magica - no amount of bad behavior will change how fluffy they are. Others simply look like ordinary people, proving that you can't always discern someone's true nature by looking at them. Johan Liebert of Monster fits this category, and he's one of the most terrifying anime villains of all time.
Do these apparently innocent bad guys take you by surprise?
Selim Bradley looks like he's just an innocent little boy, but he's actually Pride, one of the most powerful homunculi in the world of Fullmetal Alchemist: Brotherhood.
How did Sōsuke Aizen manage to trick everyone into thinking that he was a loyal member of Soul Society? By seeming to be a mild-mannered nerd who wouldn't hurt a fly. When he openly betrays Soul Society, his looks follow suit, and he appears as the villain he truly is.
Kyubey might look like an adorable pet, but they're an amoral alien who manipulates young girls into putting themselves in danger. They are trying to prevent the heat death of the universe, but the ends don't necessarily justify the means here.