Hello everyone. I have exactly the same issue - the prisoner's cage in the southern room is empty though the cage itself is locked. I opened the cage using lever, nothing happened. So I couldn't advance with the quest because without information about the stone I couldn't find it on the wall behind the altar.
I did it several times, starting from my last save of the game in Port Malan, but the prisoner was still not there.
I never was in this dungeon before. In the Journal I see only initial description of the quest, nothing about prisoners, stones etc.