Gregg Araki said in an NPR interview that he shot all of the scenes with the child actors in such a way that they did not know the sexual context of their abuse scenes, and only during editing did he make the movie appear to show children being abused or witnessing abuse.
To prepare for his role, actor Joseph Gordon-Levitt spent a week visiting cities and towns in Kansas where the book is set. Scott Heim, author of the original novel, guided him around the locations and had him meet the actual people on whom the characters are based.
Each of the youths in the film is based in part on the life of Scott Heim, the book on which the film is based. Scott claims to have seen a UFO with his family, excelled in school, and lived with his single mom after a divorce (like Brian). He announced baseball games (like Neil) and his infatuation with cosmetics and British goth pop made him the subject of death threats (like Eric).
If you look closely, the scene when the coach rests his head on Neil's chest (at 0:14:45), you can see Neil's not breathing and you cannot see his head. This is because it was an insert shot using a prop for Neil's chest so that the child actor was not aware of the sexual content that was being displayed during the production of the film.
In the scene where the boy is lying in bed, he is wearing a shirt that says, "Sex Wax and Six Packs." This is a t-shirt made for a party that is hosted annually by a notable Kansas State University Fraternity House. Kansas State University is in Manhattan, KS and the fact that the boy is wearing this shirt passed down to Hutchinson, KS shows the great deal of costume accuracy of the area.
Original novelist Scott Heim wrote a draft screenplay which he then entered into the Sundance screenwriting lab. Gregg Araki was on the judging panel and the two became friends. Eventually it was mooted that Araki himself tackle the material.
The child actors Chase Ellison and George Webster were both 9 years old during the August 2003 film shoot, portraying the boys Neil and Brian at age 8 and (in the Halloween scene) at age 10. The actor portraying Neil from age 14 (the November 1987 scenes) through age 18 was 22 years old during the August 2003 film shoot. The actor portraying Brian at age 18 was still a minor, turning 15 years old during the three week August 2003 film shoot according to his August 17, 1988, birthday.
On the 3/20/2006 "Unrated Director's Edition" Strand Releasing DVD, when the viewer selects to play the movie, a blue tinted 6 second clip from the film (at 1:35:42) of 8-year-old Neil saying "Here we go" plays before the movie actually begins. The movie starts with text on a white background.
After Brian steals the picture of his baseball team from the archives, the film cuts to Neil announcing a baseball game. He says "That's two outs, Garfield the batter. Heim on deck." Scott Heim wrote the novel on which the film is based.
In the ending credits, Bill Sage's role is simply listed as "Coach", but when Ellen McCormick, Niel's mother, takes Niel to his first Little League practice (at 0:07:15) she addresses him as Coach Heider.