The story is about a vehicle with three men in it that was fired on by a helicopter, killing two of them and seriously wounding the third. The Pentagon had said that the vehicle was attacked after ignoring warning shots, but NPR has evidence that there was not enough time between the warning and the attack for the vehicle to turn around, and that the men in the vehicle were farmers.
NPR is not claiming that there was deliberate wrongdoing. This sounds to me like the sort of accident that can happen during the confusion of battle.