OK 6 months have passed and I just encountered this bug, so it's still there (V 2.02.0749): I could see the "secret" staircase behind the closed door and couldn't figure out what I was doing wrong.
Even worse, I had another bug with this door when I came up that staircase from the other side. The first time, I could not find the switch for it to open. Only when I came back later the switch would light up.
Note: Not sure if this had any impact on this behaviour, but the second time I came up the stairs, I had Kana in my party. Before, I had never entered the dungeon with him.