Visible crew/equipment: When John is playing the piano, after the door opens by itself in the music room, there is a shot that revolves around him. If you look in the large mirror in front of the piano you can see the pole of the boom microphone reflected (behind the chandelier). (00:19:21)
Visible crew/equipment: When John puts all the evidence on Carmichael's desk, after he has accused his dead father of being a murderer, if you pay attention to the picture of Carmichael's father on his desk you can see a clear shadow of the boom microphone being pulled upwards. (01:28:48)
Visible crew/equipment: When John is recounting his story to Senator Carmichael in his office there are a number of close up reaction shots of Carmichael's face and you can see a light reflector screen in his glasses. (01:26:15)
Visible crew/equipment: After Senator Carmichael gets off the phone with Minnie he stands next to a large glass case with a model ship in it and you can see the reflection of a crew members face on the left-hand side of the glass as the camera moves in. (00:59:25)
Visible crew/equipment: During the second part of the seance, where the silver object is on the table, there is a POV shot of the spirit moving into the music room and as the camera moves through the doorway you can see the shadow of the operator cast on the floor (left side of screen). (00:49:11)
Continuity mistake: When the seance begins, there is a glass on the table that moves around from shot to shot. (00:45:39)
Visible crew/equipment: When John and Claire are listening to the music box the camera pans to Claire. If you look behind her in one of the small mirrors you can see the camera and operator reflected. (00:35:10)
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)
Visible crew/equipment: When John first enters the hidden attic room you can see the shadow of a crew member in the bottom left of the screen as the camera pulls back. (00:32:49)
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)
Visible crew/equipment: When Claire drops off some pictures for John and says she has to leave you can see the shadow of the camera operator on the door frame (right side of screen) as the camera pulls back. You can also see the boom microphone reflected in one of the small windows to the right of John's head. (00:20:33)
Visible crew/equipment: When Claire is showing John the house for the first time you can see the shadow of the camera on the tablecloth on top of the piano when John approaches it. (00:09:57)
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)
Other mistake: When John first enters the attic room, it's a roughly 8ft by 8ft small space. Yet after he opens the music box, the camera pulls back and the area is suddenly much wider.
Visible crew/equipment: When John is being shown into Senator Carmichael's office you can see the camera's shadow cast across the doors before they open. (01:24:10)
Other mistake: When Senator Carmichael enters the large building you can see a crowd of onlookers reflected in the glass windows watching the filming. (00:58:20)
Other mistake: When John is talking about the murder of the child Claire yells at him to stop but refers to him as George. George C Scott is the actor's real name. (00:57:35)
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