Elsewhere around the world, lethal force is often a last resort in such cases. Israeli police, for instance, typically use rubber bullets, water cannons and tear gas to disperse rock-throwers.
"There is no such crowd incident that will occur where the Israeli police will use live fire unless it's a critical situation where warning shots have to be fired in the air," said Israeli police spokesman Micky Rosenfeld.
Border Patrol agents since 2002 have been provided weapons that can launch pepper-spray projectiles up to 250 feet away. The agency did not provide statistics on how many times they have been used, but officials are quick to note agents along the U.S.-Mexico border operate in vastly different scenarios than authorities in other countries.
They often patrol wide swaths of desert alone — unlike protest situations elsewhere where authorities gather en masse clad in riot gear.
Experts say there's little that can be done to stop the violence, given the delicacies of the diplomacy and the fact that no international law specifically covers such instances.
"Ultimately, the politics of the wider U.S.-Mexico relationship are going to play a much bigger role than the law," said Kal Raustiala, professor of law and director of the Burkle Center for International Relations at UCLA. "The interests are just too high on both sides to let outrage from Mexico, which is totally understandable, determine the outcome here."
Officials at the Border Patrol's training academy in Artesia, N.M., refused comment on all questions about rock-throwing and use of force.
At the sprawling 220-acre desert compound, prospective agents spend at least 59 days at the academy, learning everything from immigration law to off-road driving, defense tactics and marksmanship.
"We're going to teach them ... the mechanics of the weapon that they're going to use, the weapons systems, make them good marksmen, put them in scenarios where they have to make that judgment, shoot or not shoot," said the training academy's Assistant Chief Patrol Agent James Cox.
In the latest scenario, the two smugglers were attempting to climb the fence back into Mexico, while Border Patrol agents and Nogales Police Department officers ordered them down.
"Don't worry, they can't hurt us up here!" one suspect yelled to the other. Then came the rocks.
The police officers took cover, but a Border Patrol agent opened fire through the fence on Jose Antonio Elena Rodriguez, who was shot at least seven times, according to Mexican authorities. A Mexican official with direct knowledge of the investigation said the teenager was shot in the back. The person spoke on condition of anonymity because they were not authorized to discuss details of the case.
The Border Patrol has revealed little information as probes unfold on both sides of the fence that separates Nogales, Ariz., from Nogales, Sonora. The FBI is investigating, as is standard with all Border Patrol shootings, and the agency won't comment "out of respect for the investigative process," said U.S. Customs and Border Protection spokesman Michael Friel.
Marco Gonzalez lives in Nogales, Ariz., just across the road from the border fence. He called police to report seeing suspicious men in dark clothes running through his neighborhood.
He didn't see the shooting, but he heard the gunshots. His kids thought they were fireworks.
"It affects me a lot," Gonzalez said in Spanish. "Nothing like this has happened since I've lived here. It causes a lot of fear."
The teen's mother claims her son was just walking past the area a few blocks from home and got caught in the crossfire. None of the training, political maneuvering or diplomatic tip-toeing matters to her. She just wants her boy back. She just wants answers.
"Put yourself in my place," Araceli Rodriguez told the Nogales International. "A child is what you most love in life. It's what you get up in the morning for, what you work for. They took away a piece of my heart."