Well I just found this interesting little Guardian story:

Cruise and Kidman wrecked Eyes Wide Shut, Kubrick claimed
Staff and agencies
Thursday October 5, 2006
Guardian Unlimited

Stanley Kubrick regarded Eyes Wide Shut as a "piece of shit" that had been ruined by the interference of its A-list stars, a friend of the director claimed this week. The character actor R Lee Ermey starred in Kubrick's 1987 film Full Metal Jacket and remained in close contact with the director until his death in March 1999. He described the film-maker as a "shy, timid" man who was effectively bullied by his stars, Tom Cruise and Nicole Kidman.

"Stanley called me about two weeks before he died," Ermey told Radar Online. "We had a long conversation about Eyes Wide Shut. He told me it was a piece of shit and that he was disgusted with it and that the critics were going to have him for lunch. He said Cruise and Kidman had their way with him - exactly the words he used."

...

I do like the film overall, but I can totally believe this. There are some real 'clunker' scenes, especially the "pot-fueled argument" scene, which unfortunately is crucial to the whole movie. The two main stars are definitely the worst thing about EWS.

UPDATE: The original source is here. Interesting comments about Seven as well.