Holywhippet: I completed the quest where you help out the two monks. Apparently you get a different dialogue if you use non-lethal take downs. But the first time I tried it I did use non-lethal take downs but the monks still complained about me committing murder (odd, since he didn't actually see most of them). The only thing I could think of was that I'd dumped the guy at the entrance into a bin. So I reloaded and redid the mission, this time without hiding the body. The monk then thanked me for not killing anyone. So apparently the game thinks hiding the body = killing?
You have to be careful what exactly the mission giver is asking from you. There are different levels of non-violent in this game. For example to get the best result from the Militech refugees camp where you need to do an extraction you need to ghost it and fully sneak and even non-lethal takedowns will not give you the best result. There are a couple of missions like that. Also you have to be careful with environmental interactions, i'll give another example with the corpo agent that has gone cyberpsycho in the electrified field. In order to safely take her down you'll need to either disable the electric generator first or pull her out of the water area so she doesn't get electrified as you knock her down. Most people don't bother to read what the quest giver is asking for or don't fully understand the game mechanics so we have people like you failing missions and not understanding why.
cielaqu: Using blunt weapons definitively counts as non lethal. I've dealt with cyberpsychos with a club and they were counted as alive. As for non lethal approach you also have eye mod for smart guns, mod for firearms that deal non lethal damage and two hacks.
I think the mission requies to be unnoticed.
You can kill with blunt weapons if you keep hitting the enemy after they've been knocked out, also you should avoid headshotting people with the power hammer since you can explode their heads with the overdamage(blunt weapons are non-lethal but only to a point). Best way is to experiment with the different quickhacks, weapons and grenades till you get the handle of it, this is what i did.
arugulaKhan: I've seen it go both ways. On some missions, I've hidden droves of KO'd guards in dumpsters and the "don't kill" flag didn't trip. On others, it seems, I'd look at someone the wrong way and it would.
There's definitely some bugginess going on, but you can always work around it...
The important info is generally given to you by the questgiver. The mission objectives on the side do not fully explain how you should approach some missions. The objective can be telling you to be non-lethal but the questgiver has actually asked for non-violent and taking someone in a chokehold or bashing their head till they pass out does not count as non violent.