Author Existence Failure: Just barely averted, as Kubrick delivered the final cut (without the digitally added people in the orgy sequence) to Warner Brothers just a few days before his death. And apparently Kubrick himself was prepared to insert digital people should his cut not receive an R rating.
The latter point also seems to be refuted in the documentary Stanley Kubrick: A Life in Pictures, which was released shortly after his passing. Tom Cruise and Nicole Kidman speak in a very entranced manner about Stanley (with Cruise providing narration for the documentary), and they sound as though they were just as subservient to and bemused by his perfectionism as anyone.
No Export for You: Kubrick arranged to have the novella that the film was based upon kept from getting an english language release until after the film's release in order to ensure the film's plot does not get spoiled.
Throw It In: Two musical cases. The choreographer played Jocelyn Pook's "Backwards Priests" on the set rehearsing the masked ball intro. Kubrick incorporated the song on the scene and called Pook to do the original score. Kubrick also allowed Nicole Kidman to listen to some music in order to liven up for nude scenes - and liked her choice of Chris Isaak enough to incorporate it in the movie and its advertisements.
What Could Have Been: Harrison Ford was Kubrick's first choice for the lead and reportedly wished that he had gotten Ford in a comment made shortly before his death.