There seems to be a lot of argument over whether the assassins that attack Corvo, and the empress and kidnap Emily in the prologue count towards any of these achievements. The achievements all say "all missions after the prologue," so I would assume not, but I've not heard any official statement on the matter.
What exactly is the relationship between kills and "dead or unconscious bodies found?" I know that anything that happens to an unconscious target after you knock him/her out is counted against the player, but the one time I know for sure I screwed this up, the mission stats said I had a kill so I restarted. Is there any way that someone you knocked out could somehow, and count against you for the clean hands achievement, but not be listed as a kill in your post-mission stats screen? Could "dead or unconscious bodies found" possibly include being found and devoured by rats? I mean, I was extremely careful, borderline paranoid because I'd heard of all the trouble people were having with these achievements, all my missions have both "didn't kill anyone" and "ghost" checked, and somehow I still missed out.
Given that all my missions are marked with no-kills and ghost, I can only assume that I somehow accidentally killed someone in the space between missions. The only between-mission potential targets that come to mind, though, are the weepers in the sewers beneath the Hound Pits Pub between missions 2 and 3. I had heard all kinds of things about these two, so I was ridiculously careful to make absolutely sure that nothing could possibly happen to either one of them, and I even got a message from Piero later thanking me for providing him with a live weeper "specimen," so I'm pretty sure I didn't somehow accidentally kill them. But anything is possible.
In mission 7, I played around with various ways to take out Daud, and I really liked his post-combat speech for my low chaos run, but I didn't want to be detected. So, I decided to stick a sticky grenade on him and run behind cover. He exploded and teleported to his post-fight location without ever having seen me. Could that have counted against me for the "Clean Hands" achievement, even though it wasn't listed as a kill in my mission stats?
I've heard a lot about the situation with Lockjaw and Granny Rags in mission 7. Most people seem to advocate stopping time, stealing the key from Granny, and getting the Hell out of there. Seems like good advice, but I didn't quite follow it. I wanted the rune in her shrine, so I stopped time, grabbed the key, ran up to her little bedroom/kitchen thing, unlocked the door to the back room and shut it behind me. That way when she realized the key was missing and started her whole "Surprise, I'm a witch!" routine, she wouldn't spot me. Then I grabbed the rune, stopped time again, freed Slackjaw, and then got the Hell out of there. I figured he would run for it, but instead he started fighting Granny. I didn't stick around to see what happened, but I assume she probably killed him. Still, I didn't get any kills listed on my post-mission stats screen, so I assumed everything was legit. Is it possible that letting those two fight it out counted against me?
Actually, on that note, I let a couple NPCs that I wasn't involved with die. Like the two overseers killing one of their own who had come down with the plague in mission 2, and the weepers attacking thugs in the Distillery in mission 3. Could those have counted against me?
Speaking of the Distillery, does poisoning Lockjaw's bootleg elixir still for Granny Rags in mission 2 count against you? I would assume it doesn't because otherwise you wouldn't end up with the scenario with the two of them in mission 7, and some people have gotten through that scenario and still gotten Clean Hands.
Long post is long, but I that's about all I can think to ask at the moment. A couple of these are things I could test relatively easy, but I'm going to be pretty busy in the next couple months, and I won't have a lot of time. And quite frankly, even if I did, I don't have the energy to go through and ghost the last three missions, much less the entire game again without any guarantee that it would accomplish anything. A couple of people have posted the idea already, but it would have REALLY helped to have had some stats on the things that you've done between missions as well as during missions just so people would have some idea why they aren't getting the achievements they worked for.