The scene in the movie, where on the way to Cecilia's funeral, the graveyard workers are holding a strike protest at the entrance. Mr. Lisbon just solemnly gets out of the car, talks to them, and they move aside, stunned about the circumstances of his daughter's death.
Mr. Lisbon going into Cecilia's room, possibly imagines her ghost, and discovers that the window where she plunged to her death is open. Closing the window, he clearly bends his head down in distress. Then he finds Bonnie, reassuring him that the yard workers moved the gate where Cecilia impaled herself.
Lux's final scene. The boys are too excited at the prospect of rescuing the girls that they don't really seem to notice that Lux is incredibly glum, as if she knows already what happened to her sisters and knows she's next.
The scene where the boys make contact with the girls and they play music on their recorders over the phone line. While the book conceals how the Lisbon girls exactly feel about it, the movie drops some hint. The boys are glad, while the girls are glad, yet very solemn, as if they know this is their final moment together.
Portraying 14-year-old Lux as a Ms. Fanservice who Really Gets Around may come across as awkward to modern readers. Though it's pretty clear she acts this way as a reaction to her ultraconservative mother, she'd still likely be at least two years older if she were created today.
The minor character Joe Larson, a boy with Down Syndrome, is repeatedly described as a "retard" and a "mongoloid" by the narrator. Even allowing for the fact that the narrator is a tactless teenage boy, this would not fly today.