That was kind of intended. Warren will only appear at the Sanctum, after you talk to him in the upper garden. (maybe this was a bad idea)
But you should be able to walk back to the upper garden and talk to him, to fix this issue.
Maybe I should change this, so it is not possible to advance, without talking to him first.
Edit: Ahhh I think I know now what you mean. I didn't think of that! I will look into a fix for that.