Income taxes are pay as you go. If you don't have enough withheld during the year (or make sufficient estimated payments) so that you owe more than $1000 when you file, you can be assessed a penalty for underpayment throughout the year, even if you pay in full when you file. See this for more,
https://tax.illinois.gov/research/publications/pubs/illinois-estimated-payments-requirements-for-ind...
If you did not owe more than $1000, the letter may have been sent in error. Write to the office that sent the notice with your explanation and copies of any relevant documents.
