Nah both of them have no switches attched to them.
But he was in your time in the story just not afetr you defeated teh boss and compelted the story?
Also can you put him into your party from the guild or home wher you switch party members?
Yeah, small tileset error, will fix taht as well.
Edit: I actually think I now why, its because of the party order save most likely. It saved your party when starting the quest (Which was only Nana) so it now laoded that saved party after finishing the quest.