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.
Creator Backlash: Disputed. R. Lee Ermey has said that Kubrick confided to him that he thought the film was "a piece of shit" and that he allowed Cruise and Kidman too much creative control, but Kubrick never openly said anything (for obvious reasons) and his producers said he was very pleased with the result. Todd Field, who starred as Nick the piano player, vigorously disputed Ermey's allegation, and Kubrick's daughter Katharina mentioned that "he was proud of most of his films, but he was very proud of Eyes Wide Shut" in a Reddit Q&A. (Really, the very concept of actors having too much creative control in a Stanley Kubrick film is so ludicrous as to make Alien Space Bats look plausible.)
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.