I've been doing some Google searches and it seems I'm not alone in this. Mission 3. Was going to kill the Pendleton twins, but Slackjaw wants me to find out what happened to his gang member over at the scientist's house. I go in, put everyone to sleep, find the slain gang member and take the audiograph clue, and then I head back to the Distillery. However, halfway between entering the zone and actually getting to the building, the game tells me I've failed the mission, and Slackjaw tries to kill me. Anybody else have this problem, and if so, have you fixed it?
I've been playing more or less non-lethally. When the weepers escaped in the beginning of the mission, I left them alone. The game doesn't tell me I've failed the mission until I've crossed a certain point in the path leading up to the distillery building - it just suddenly goes wrong, whether I sneak in or just waltz on through. .
I was running into some issues with this mission as well. I made the deal with Slackjaw to find out about his man. Slackjaw's minions inside the distillery building were non-hostile to me, but all of the ones directly outside the building still were trying to kill me. I died, reloaded a save after I had accepted the mission from Slackjaw, and all the sudden he was trying to kill me also. Had to reload a previous save and just keep stealthing everywhere even after accepting the mission.
I had part of that mission fail (had to reload) because I opened the door inside the distillery that has the three or four weepers in it. They got pissed at me for doing that, evidently, heh. Could that have been it? I did the poison run for Granny Rags, too, and was able to do everything Slackjaw wanted successfully.
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