Are the quests showing as completed in your journal? If not, did you speak to the NPC's again after all your fights until they completely leave you? Forget if there was an additional cutscene before you talk to Minfilia again at the end to close them out or not---but there was a separate CS with her at the end for each line that you had to do before she moved on. If you ran them sort of parallel, when you talked to her you had to pick one to watch, then talk to her again to close the other one.