The injured employee was working atop a hopper car, replacing running board bolts. He was wearing a harness and lanyard, but was not secured to the car. At the same time, a second Team Member (TM) was preparing to utilize the overhead crane. Before operating the crane, this second TM reviewed the permit that was attached to the crane control showing the injured employee to be working atop said hopper car. He went to the car the employee was reported to be working on, and did not see him. He then looked at other cars the crane would be passing over, and did not identify anyone working atop those cars either. At this point, the second TM began to move the crane west (away from the employee) and secured the welding machine to be moved. Once the machine was attached and lifted off the ground, the load was moved east (toward the employee). As the crane passed over the car on which the injured employee was working, he fell approximately 16 feet to the ground fracturing both ankles and a leg.