"I dunno," the Doctor admits, as he looks over at the ghost. "Part of it might be that. But then again, one of the ghosts I saw was a ghost of somebody already here."

Just in a different time. It was Clara at the moment of her death that haunted him for a few days, while alive-and-breathing Clara in this world continued to exist.

"Of course, it could be that a couple of incidents happened at the same time. The Porter might be able to plan for one instance of catastrophic failure, but maybe not two."