Yes, you have to file two state income tax returns:
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For IL: File an IL Nonresident income tax return and since you are preparing a nonresident return solely to recover erroneous tax withholdings, enter 0 on the screen that asks for the amount of income earned in that state. This will eliminate your tax liability for that state, resulting in a full refund.
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For WI: You need to answer that all your income was earned in WI and you will pay the appropriate income tax.
Wisconsin has a state reciprocal agreements with Illinois so you don't pay sate income taxes to Illinois. Submit the following form to your employer so IL taxes are not withheld in the future: IL-W-5-NR
Additional information:
