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Were the penalties for a personal return or for an 1120S filed for an S-corp? The S-corp filing deadline was not extended. It was still due on March 15 for an S-corp using the calendar year.
Or a Partnership form 1065 ? All of the business returns that had a due date of 3/15/2020 either had to be filed or an extension form 7004 filed otherwise the return is late and the penalties will be accessed. ONLY returns with a due date of 4/1/2020 or later were automatically extended to 7/15/2020.
NOW if this is your first transgression then respond to the notice and beg forgiveness of the penalty and use the "I thought all returns were extended" excuse ... say you are sorry and then file the business return ASAP.
If you are paying quarterly estimated taxes you will find that the Feds like to get their money spread equally throughout the year. If you skip a quarter or do not pay until the last quarter they will charge you a penalty for underpayment. https://www.irs.gov/businesses/small-businesses-self-employed/estimated-taxes
if this is in regard to your personal return, evidently you did not have enough withheld and/or paid in on estimate to meet the minimum requirements to avoid underpayment of estimated tax penalties. we can not see your returns
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