If the IRS is saying you never filed, you can call customer support for help in proving you did file a return.
If the IRS is saying you filed late, they are right. The deadline for C and S-corp returns is March 15, not April 15. This year, the IRS extended all deadlines that fell after April 1 to July 15, but that means the March 15 corporate filing deadline was not extended. The penalty for late filing an S-corp or LLC return is $195 per month per shareholder or member.
Here is how to request a penalty abatement.
https://www.irs.gov/businesses/small-businesses-self-employed/penalty-relief-due-to-first-time-penal...
