So far, I've seen two glitches with Alan in Arefu that are kind of entertaining. If you convince Vance to send someone to protect Arefu, leave, then come back (Alan disappears to respawn in Arefu) and then slaughter the Family, when you return to Arefu he'll have killed everyone. This did happen when I had Charon in my party, and to be honest I can't be 100% sure that it wasn't Charon shooting at people through the floor of the bridge (since he was out of my sight the whole time I was running to Arefu). But I can tell you that when I arrived and killed Alan, I saw that everyone else had already been killed, and he was the only one standing when I arrived.
Second glitch, when arriving in Arefu after convincing Vance to protect them, going into the previously abandoned house Alan came down the stairs and walked out the door. I grabbed the loot and exited as well to see him walking away from Arefu. I decided to follow and sure enough, he made a bee-line straight for the Bed and Breakfast. He summarily got his ass handed to him and I picked up the pieces.