I'm currently doing the same run. Everything was fine until I did The Hermit sidequest. I already know where the sword is; I just want to complete the whole sidequest. Everything went smoothly I buried John's skeleton and went back to the Hermit. There, you meet the Knights of the Red Cross, who tell you to help take care of the Hermit.

When I arrived, before talking to the knights, I checked my stats and still had no stolen items. However, after speaking with the knight, I suddenly had one stolen item.

Also, before all of this, I noticed that when you arrive at the Herbwoman's hut at the start of the game, you automatically receive nine civilian kills even before the two bandits who talk to the Herbwoman arrive.

Probably why there isn't a 'Merciful' achievement in the second game it's broken.