The scene where Isabelle's hair catches fire happened unplanned. Eva Green was supposed to lean forward and kiss Matthew goodnight but accidentally caught her hair on fire on the candle on the table. She didn't let it worry her and acted so natural that Bernardo Bertolucci decided to leave it in as he felt it perfectly anticipated the theme that things are about to get a bit crazy.
To make the actors feel comfortable and natural in the film's nude scenes, the director Bernardo Bertolucci would encourage them to be nude long before the actual shot. Source: Director's commentary on DVD
There were scenes in the script depicting much more blatant sexual relations between the characters of Matthew and Theo, but they were not filmed. Director Bernardo Bertolucci said, "The gay sex was in the first script, but I had a feeling that it was just too much stuff. It became redundant." Actor Michael Pitt said in an interview, "It was in the script and it's what I'd signed to do. But they said we weren't going to do that."
Director Bernardo Bertolucci was so impressed how the actors so naturally acted naked, he penned an uncredited lengthy extra scene in the script where all three main actors are overtly nude. It ended up on the cutting room floor.