Why did the boy call 911?

At the end of the movie, Sean (Kevin Bacon) tells Jimmy (Sean Penn) that the "Silent Ray" and his friend John O'Shea had found "Just Ray's" gun and that they were playing around with it. In their confession, they stated, according to Sean, that they saw a car approach and they just wanted to scare the person driving the car, which happened to be Katie's car (the girl that was murdered.) Since she and the "Silent Ray's" brother Brendan were in love and were planning to leave for Las Vegas the next day permanently, it's a reasonable assumption she was in the neighborhood going to Brendan's. Jimmy tells the detectives at one point that she looked at him like she was saying goodbye...

The 2 boys also supposedly stated that when they tried to scare Katie, the gun went off and they subsequently chased her to keep her from telling anyone. You can infer from the actions of the of John when Brendan figures out that his brother and John killed Katie that things could have easily gone out of control when they were chasing Katie. He beat her with a hockey stick, after all. If this were a true story or the writer was trying to convey some authenticity regarding how these boys would react, it is reasonable to assume that one or both of the boys felt remorse and/or fear after the murder, particularly because they knew the victim.

Stepping out of the story and back to the reality of a writer, this is really just the "Smoking Gun" that allows Kevin Bacon's character to crack the case. The author either didn't think the audience would question WHY the boys would call or thought their actions were plausible enough that no one would notice. Good call-out! I didn't catch it until I watched it again after reading your post!

Here is the phone call transcript :

“There’s like this car with blood in it and, ah, the door’s open, and, ah—” 
The 911 operator broke in and said, “What’s the location of the car?” 
“In the Flats,” the kid said. “By Pen Park. Me and my friend found it.” 
“Is there a street address?” 
“Sydney Street,” the kid expelled into the phone. 
“There’s blood in there and the door’s open.”
“What’s your name, son?” 
“He wants to know her name,” the kid said to his friend. “Called me ‘son.’” 
“Son?” the operator said. “I said your name. What’s your name?” 
We’re so fucking outta here, man,” the kid said. “Good luck.”

My guess would be that the persons who called want the body to be found. My other guess is that the writer use the phone and specifically the caller's slip to pinpoint to the murderer.

The caller misunderstood the dispatcher's question, he thinks the dispatcher wants to know the victim's name and says "her", at this point, he has no way to know the victim is a girl unless he is the perpetrator.