Like Lou S. noted, to be eligible to file under the DFVCP, Form 5500 annual reporting must be required under Title I of ERISA. The DFVCP program does not apply to plans covering only self-employed individuals or sole owners (including spouses). Reporting for these plans is only required by the Internal Revenue Code and are not subject to Title I of ERISA. These types of plans may be able to file with the IRS under Rev. Proc. 2015-32.
Because you know the amount of the penalty that may be assessed, presumably you received a Notice of Intent to Assess a Penalty (that is, a CP 283 Notice), which will disqualify the Plan from using the DFVCP or the IRS Rev. Proce 2015-32 program. If, on the other hand, you simply received a Notice of Failure to File without the assessment (that is, a CP 403 or CP 406 Notice), you could still use the programs.
If you don't qualify for either of the Programs, like Dare S. states, you should contact an attorney (or your CPA advisor)) and seek an abatement of the penalty. You should make sure to do this before the time for a response that is contained in the notice runs out. Generally, a full waiver is only granted if one of the reasonable cause requirements are met; (fire, casualty, natural disaster, etc.; inability to obtain records, death, serious illness, incapacity, etc., or some other reasons establishing that the plan sponsor used all ordinary business care and prudence to meet its filing obligations but, despite its best efforts, failed to meet the file standards). Not sure where miscommunication comes in but in recent years, the IRS has become less accepting of other reasons (for 2022, COVID would be another potential reasonable cause). Hopefully, your attorney (or CPA advisor) knows how to couch your specific facts.
Just my thoughts so DO NOT take my ramblings as advice.