Kinda the same with Dishonored. I finished the entire game and wondered why I didn't get the non-lethal award.
Turns out that the tutorial that specifically told me to kill 2 guards in the beginning of the game counted.
I did this same thing in Undertale. I "killed" the training dummy in the tutorial and had 5xp the entire game. I was unable to do a pacifist run. I later found out you can't do pacifist on your first run anyways so it kinda sorted itself out.
