I just beat the game without killing anyone in the game and clean hands did not go off. I checked my stats for each mission and each one says no one killed checked.

Did you (SPOILERS)

Please use spoiler tags if you are divulging quest details. Though these may be minor details, it is a good habit to get into. Use the BB Special Code and choose Spoiler.

Thank you.

I feel like a chastised child. Sorry Sir. Won't happen again.

I think steam is just the problem with the achievements. Sometimes I'll just be hiding and suddenly I get an achievement for something I did five minutes ago.

When I got the clean hands achievement, the pop up didn't come till I returned to the menu.

Also:

turns over rock

You are forgiven.

I did not kill Granny Rags, I stole her key and ran past that whole business since it seemed there was no way to not kill her or Slackjaw. (which is a failure on the game's part, in my opinion.)

I did not poison the distillery, I didn't kill anyone!

Do the guards eaten by rats in the sewer count? There's no way to prevent them from being eaten! The door is barred! The only way past is to climb above them, and then they walk into their death. Is that really my downfall here? Those two guards in the very beginning of the game, that I can't do anything about?

..if that's the case I give up on it altogether.

Number one in that 2 point list adds to the player's chaos, but it does not count as a kill. Also, the second point, those NPC's cannot be killed and there for do not add to the kill count.