Can confirm this is still a problem. Recently finished shrine tales, and after getting 50 Closeness with Ibaraki and doing his quest, I got a broken quest bubble stuck above my head.
Update: found a way to get rid of it. After getting 50 Closeness with Ibaraki again, I Asked him to "Sing in Ellnia" or something like that. Then some quest requirement completed for a "Greetings from Zipangu" quest which is now listed as completed in the lightbulb icon on the side of my screen. Although I can't complete the quest from there. When I click it Ibaraki wants me to wait 30 minutes before Asking him for something else. At least there's no more lightbulb above my head!