My wife denied visa for unlawful presence but was waiting...?

My wife was denied a visa because of unlawful presence for 2002 but during that time she was waiting for status change and has letters from USCIS to prove it. She was told not to leave the U.S. at that time. What can we do to show the consular that my wife was doing the right thing and was not unlawfully present? Do we need to do an appeal or demand action from the consular for misjudgement?