The ghost of Hugh Crain was originally supposed to emerge from the fireplace and try to attack Nell. The clip of Crain's ghost emerging from the fireplace is seen in the behind the scenes special of "The Haunting" hosted by Catherine Zeta-Jones. In the theatrical cut, Hugh Crain's ghost comes out of the defaced portrait and hovers down the staircase to Nell.
This remake of The Haunting (1963) was going to be entitled "The Haunting of Hill House" which was the original novel title. It was shortened back to "The Haunting" to avoid confusion with House on Haunted Hill (1999).
At the time of its release, it was widely rumored that Steven Spielberg either directed some scenes or participated in post production because he didn't like the rough cut he saw. This was, however, never confirmed.
Deleted scenes shown in theatrical trailers and TV commercials for "The Haunting", but not included in the final cut of the film, include a scene where Nell and Theo open up doors to the house while exploring and they find brick walls in the doorway to prevent them from entering and a scene with Theo in Nell's bedroom, shortly before Dr. Marrow admits the truth about his experiment, with Theo saying "As soon as I turn out the light, my heart starts pounding."
The trivia items below may give away important plot points.
Eleanor Vance and Luke Sanderson are the two guests who die in Hill House and are only characters to close the main hall doors that are later used to trap the ghost of Hugh Crain. Nell closes one of the doors when she tells Theo about purgatory and Luke shuts the door to give Nell some privacy with her tests when he leaves.
The shooting script used during filming saw more scenes with Hill House's caretakers, the Dudleys. In one scene, when Marrow is talking to Nell alone in the greenhouse, Mr. Dudley enters and tells Nell about where Hugh Crain's first wife Rene hung herself before he goes off to clean the paint letters from the Hugh Crain portrait. In another, after Nell finds out Dr. Marrow isn't behind the creepy incidents at Hill House, Nell looks out the window to see the Dudleys about the leave and Mr. Dudley holds the gate open as an invitation for her to go with them. When Nell doesn't join them, Mrs. Dudley smiles and she closes the gate so her husband can lock it.
In the original shooting script, David Marrow's first name was actually Jim. The name David is taken from an omitted character from the script named David Watts, who was a guest Marrow invites to Hill House for the study. The absence of Watts takes up most of the shooting script when Nell sees Watts's car drive up and she later finds the keys to his Toyota by the fireplace, but Watts himself doesn't arrive inside the house and the guests split up to look for him. Near the end, when Marrow, Theo and Luke look for Nell when she re-enters Hill House, they find the dead body of Watts held in the hand of the man statue in the greenhouse pool.
In the movie, David Marrow talks to his boss Malcolm about his research on the dynamics of fear. In the shooting script, Malcolm allows Marrow to go to Hill House because it will give him the study and results he needs for the last chapter of his book entitled "Fear and Performance". In the script's alternate ending, Marrow publishes the book and dedicates it in memory of those who died in Hill House: Rene Crain, Carolyn Crain, Eleanor Vance and Luke Sanderson. David Marrow's book being published is cut out of the movie, though Malcolm does say "fear and performance" to David when originally trying to talk him out of doing his research.
In the theatrical trailer, there is a scene where Nell asks Theo if she ever kept something to herself because she was afraid and Theo says, "All the time." This is taken from a deleted scene mentioned in the original shooting script used during filming where Theo and Nell are in Theo's rooms, having drinks and Theo is painting Nell's toenails.
In the script, when Hugh Crain's ghost is closing the doors of Hill House to prevent the guests from leaving, Nell watches and repeats Mrs. Dudley's line, "In the night. In the dark.", in between scenes where doors to the house slam shut and lock on their own. In the film, Nell says "In the dark" ahead of Mrs. Dudley when she repeats her quote to Theo in her bedroom for comedic effect.