I just found Alice at the Evil shrine. Before checking her, my save menu says I have finished 49 quests, which seems right. It's 54 minus two three that I've missed, minus the relic one as I'm still short of one relic, minus the hero one.
But when I check Alice, the dialog says I've finished 51 quests. Then the characters say their lines about how many quests they've done and how much XP they get.
After that, the whole thing starts over, I get the 51/54 notification again, everybody says their lines again, and they indeed get the XP twice.