Felt weird when I found the stowaways that were stealing greenhouse stuff in Fairport, the sheriff came down, the dialogue turned "okay we gonna kill you" - then they didn't. Even when I attacked one of the guards or the main girl the others would not attack. I didn't think anything of it, then later in the game doing the main relay quest and went to sneak up to kill a protectorate soldier... no sneak attack. Only pickpocket.
I was able to kill the boss there but this takes all the challenge out of the game and will probably bug something later. When I "trespass" within their territory they just look at me. I can't sneak attack anyone, if I hit them they'll finally defend themselves but their allies just watch. Really hoping for a patch.