Wander the castle widely. I found that when I first got there, some companions were in other parts of the castle exploring or talking to other NPCs.
They are always marked at the map where they are suposed to be at the time of the game. But yes most of the Followers are not on the usal place when you come to skyhold, but they are marked on the map where they are suposed to be at the state of the game.
I think i have found the solution. take the companion that you cant find, with you out in the field and then return. It made mine come back to the surface.
