UPDATED: August 25, 2020 - The IRS has temporarily suspended the issuance of notices CP501, CP503, and CP504 to taxpayers who may have a balance due on their taxes, as a delay between taxes being paid and recognized has created some confusion among those receiving a notice after paying taxes. You can read more on the IRS website.
ORIGINAL POST: August 20, 2020 – The IRS has indicated they are behind in processing payments due to Covid-19—although the return may have been processed, many of the checks mailed either with or without a tax return have not been cashed.
As a result, many taxpayers have received notices recently indicating they have a balance due on their account when in fact they have already made the payment. Also, payments made will be posted according to the received date rather than the date on which they are processed.
The IRS has indicated that taxpayers who have already submitted a payment should not stop payment and re-issue a check as this action may incur unnecessary penalties and interest. Instead, they should wait until the IRS processes their payment. If taxpayers receive a notice regarding this but have confirmed the payment has been made, no further action is needed.