The 1120-S return was due on 3/15/2020 ... so if you did not put it on extension by 3/15 (which got you to 9/15 to file) then you have filed LATE. The IRS is correct.
Only returns that had a 4/15/2020 due date were extended to July on 3/23/20 ( 8 days after your return was due) but they did not apply to returns that should have already been filed or on extension.
Per the IRS:
The 2019 income tax filing and payment deadlines for all taxpayers who file and pay their Federal income taxes on April 15, 2020, are automatically extended until July 15, 2020. This relief applies to all individual returns, trusts, and corporations. This relief is automatic, taxpayers do not need to file any additional forms or call the IRS to qualify.
https://www.irs.gov/newsroom/payment-deadline-extended-to-july-15-2020#:~:text=The%20Treasury%20Depa....
