SAN DIEGO—A man accused of piloting a boat overloaded with illegal immigrants that crashed into rocks off San Diego’s coast and killed three people kneed a U.S. Border Patrol agent in the face who was trying to put a leg shackle on him on the beach, authorities said. Investigators said in an affidavit filed Tuesday in federal court in San Diego that the agent was not seriously injured but the hit left a red mark on his forehead. A total of 33 people were pulled from the water after the 40-foot trawling-style boat smashed into rocks and broke apart Sunday, tossing people into the rough sea off Cabrillo National Monument. Besides the three who died, two others were still hospitalized, including one in critical condition. Investigators say Antonio Hurtado, a U.S. citizen, was piloting the boat, and he was arrested on suspicion of bringing in or harboring illegal immigrants and …