It sounds like your state withholdings were not assessed correctly by your employer. Was there a change in payroll services or a change in payroll systems in 2024?
Iowa and Illinois have a reciprocal agreement for individual income tax purposes. Any wages or salary made by an Illinois resident working in Iowa is taxable only to Illinois and not to Iowa.
You will file an Iowa nonresident state income tax return to receive a refund of taxes that were withheld to Iowa.
You will file an Illinois resident state income tax return but you will have a balance due. Enclose a letter to Illinois asking for 60-90 days to pay the balance due. Hopefully, that will be enough time for the Iowa refund to be received.
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