You need to contact the IRS since it appears that you did everything properly to pay the taxes owed and on time. The IRS is certainly not infallible and they do make mistakes.
If there is a phone number on the notice you received then call that number and speak directly with an agent.
If there is not a phone number, then use this procedure to contact the IRS -
Call the IRS: 1-800-829-1040 hours 7 AM - 7 PM local time Monday-Friday
When calling the IRS do NOT choose the first option re: "Refund", or it will send you to an automated phone line.
So after first choosing your language, then do NOT choose Option 1 (refund info). Choose option 2 for "personal income tax" instead.
Then press 1 for "form, tax history, or payment".
Then press 3 "for all other questions."
Then press 2 "for all other questions."
- When it asks you to enter your SSN or EIN to access your account information, don't enter anything.
- After it asks twice, you will get another menu.
Press 2 for personal or individual tax questions.
Then press 3 for all other inquiries
It should then transfer you to an agent.
