I've just finished the game without killing anyone, played through the whole thing not using mission select. Did the first granny rags mission about the gentlemen callers but didn't infect the elixir. Did all non lethal options but still not achieveable?

Did you do anything to Granny during the Flooded City? Apparently there's a glitch and even if you
choke her / sleep dart her, the game still counts it as a kill even if you don't see it listed as such on
the post-mission stats screen.

Damn... I put her to sleep... I guess that was it :/

Same issue as you except I didn't choke/sleepdart Granny Rags, just stole her key and legged it. Only received the Shadow achievement upon beating the game. Is there any other known "glitches" such as these where you won't get it even with 0 hostiles/friendly kills on every mission?