This seems to be a problem between your employer and you since it is it's responsible for doing timely antidiscrimination testing. As a HCE your contributions would not be deductible so you will owe more taxes and penalties. file an amended return and pay the additional taxes. The IRS will send you a notice about penalties. The notice will contain instructions of how to get the penalties abated.
You may be given one of the following types of penalty relief depending on the penalty:
1) First Time Penalty Abate and Administrative Waiver
2) Reasonable Cause
see this link for how to request penalty relief
https://www.irs.gov/payments/penalty-relief#eligible
if the IRS denies relief talk to your employer to see if they'll do anything to make you whole. If not, your only option would be to consult an attorney to see if your employer could be held liable but the costs would probably be prohibitive but you can always call to get an idea.
