I have the exact same issue with my current game. The same thing applies if I try to attack a friendly NPC, they won't turn hostile. I caused the bug to happen when I was doing the Endless Paths of Od Nua Level 11(or at least this is the first time it happened). I attacked the passive spores in the NE section because I've had issues in the past where I needed to exit and rest, and that group was alive and hostile blocking my way. They never turned aggressive on me, and everything since has been broken.
