I'm not sure about this but... did the story imply that Nagi got raped by an older omega woman? Considering this is an ABO world, having a grown adult prey on a teenaged kid and using pheromones to their advantage to induce them into having sex seems to be what happened to Nagi. And then there's that bit about him imagining Nao calling him tainted if he were to find out about this. That's just sad.