I've come across this situation twice. I'll be playing silently, hiding bodies if I must and being generally sneaky. While playing, i'll make a mistake and cause the the AI to go into an alert state. So i'll reload a previous manual save and for some odd reason, the AI will immediately go into an alerted frenzy again. I swear i'm not crazy, and i'm not loading up an autosave. My most recent encounter with this was on The Royal Physician mission. I also received the Manipulator achievement without ever trying. It just randomly popped while playing and i'm not quite sure, what i'd done to cause it to activate. Weird stuff.
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