I just finished the Battle of Bunker Hill quest and the resident NPCs are all cowering as if the battle was still going on. I've fast-traveled in and out several times since then and they're still doing it.

Oh, and one of the BoS Paladins seems to have taken up permanent residence.

Oddly enough the characters can all be interacted with normally.

Anyone have a fix for this?

I had the same happen in my last game. (In this one I've yet to do The Battle of Bunker Hill.) I tried sleeping, relaunching the game, etc and some NPCs (the doctor) stayed cowering and the BoS Paladin stayed around for a long time but eventually left and nearly everyone came out of cowering except one NPC at the doctor's stand. Perhaps someone else will have some advice.

Same thing happened to me. I figured out you can fix it by console commands.

Type: stopquest ef21c

Leave the location(fastravell away) and come back.