Warning shots
It's interesting that only the Jerusalem Post article refers to a "warning shot." The quotes in the article attributed to the military imply that they just up and shot at them.
Israeli military sources said soldiers opened fire at a group of people who broke through a security fence outside the base that borders on Kalandiya refugee camp, between Jerusalem and the West Bank city of Ramallah, striking one of them.
"The Israeli army expresses regret about the boy's death and has opened an investigation into the incident," a military official said.
I found nothing on this incident so far on the Israeli Defense website, so I don't know the original source of the "warning shot" scenario.