When the Internal Revenue Service lifts a penalty, it is called Penalty Abatement.
One of the few reliable ways to get a penalty abated is IRS error. If the IRS was in the wrong in this situation, both the penalty and the resulting interest on that penalty can be refunded to you.
You will need to file a Form 843 requesting an abatement of the penalty. If possible, you should get an attorney to assist you with this matter to increase your chance of success.