Sometimes a companion will take a route that will lead it into a "hostile territory" when not directed to do so by player movement. I don't mean that the player has moved toward hostile territory but is trying to position "just outside" it... I mean, in no way, shape, or form, did the player move toward this hostile territory (in fact, the last time this occurred to me I was in the inventory and did not click on the world for certain). Interacting with something else, or moving in a direction that should not cause the companion to do so causes the companion to take a long and nonsensical route and trigger hostile characters.
This isn't a big deal in an alpha/beta in classic mode, but if this never gets fixed, I would never play honour mode, that's for sure.