The S-corp was not automatically extended ... you had to file an extension by 3/16 to get to 9/15 to file the S-corp return and there are no second extensions for businesses.
The auto extension (for personal returns and those returns with a 4/15 filing deadline) to the covid date of 7/15 was done a couple of weeks AFTER the 3/16 deadline when all businesses were to have their extensions already filed. Even then, if you still needed more time to file after 7/15 you had to file an extension to get to the 10/15 deadline.
If you got a late filing penalty and this is the first one your business has gotten then write back and use the " I didn't understand about the filing deadline changes" for an excuse and promise to never do it again and they will usually abate the penalty for the first offence ... this will not work a second time so pay attention going forward.
