Medicare's first public effort to identify hospitals with patient safety problems has pinpointed many prestigious teaching hospitals in Boston and around the nation, raising concerns about quality at these places but also bolstering objections that the government's measurements are skewed. Massachusetts General Hospital and Beth Israel Deaconess Medical Center, both affiliated with Harvard Medical School; and Boston Medical Center, affiliated with Boston University, were among those having substantially more complications than the average hospital, according to data evaluated by the Medicare program.