I had this exact problem where I knocked out the leader goblin with the knock-out attack and they ran away as well. Then when I tried to talk to them with 1 character it didn't work, then another character and that didn't work either. From then on it was always broken for those 2 characters (maybe mc and wyll just like you actually). No matter if I killed the mc and revived it would not fix it. I just reloaded from before I attacked them at the windmill.
