Continuity mistake: When John is pushing his car through the snow (with his wife and daughter) you can see the snow on the road is thick and solid. When John enters the phone box the snow suddenly becomes very slushy and muddy. (00:01:30)
Continuity mistake: When John is removing the shelves, in front of the hidden door, almost all the clutter vanishes after he removes the first shelf. It would have taken him a lot longer. (00:30:27)
Continuity mistake: When John finds the diary in the hidden attic room the date on the front reads "January 1909", however later on when Claire reads it she says "January 4th 1909." (00:33:55 - 00:36:38)
Continuity mistake: When the seance begins, there is a glass on the table that moves around from shot to shot. (00:45:39)
Continuity mistake: The roof of the Chessman House changes, going from having a middle roof to no roof in the middle.
Answer: It was implied to be his "spirit" or "soul" that John saw.
TedStixon