I experienced similar situations.
In Oct., I took flights Japanese domestic flights by ANA. (NGO-ISG, ISG-HND)
I applied A3 number at check-in and confirmed on boarding passes (which A3 number printed), but miles from the ANA flights were not appeared, so I claimed miles after two weeks.
I think, due to maintenance issues, the miles have not applied. I suppose you need to claim missing miles after 14 days from the flight date.