So my son forgot to change his address last year with his work who took out both MN and WI taxes but he changed it early last year when doing his taxes last year. He lived in MN the whole year but his work took out taxes ~$5 on about $6261 'made' there. It says he owes WI $236 because of this. Minnesota wants to know his WI taxable income which I think is $241 based on the WI form and his income is then the $6261 which then bascially gets him that $236 back from MN. or am I missing something?
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File a non-resident Wisconsin tax return and report $0 income since your son did not live or work in Wisconsin and his employer took taxes out by mistake.
That will change your Minnesota taxes. You will not get any credit for tax paid to Wisconsin because there is no tax on $0 income.
On the screen “Wisconsin Salary Allocation,” enter $0 for Wisconsin.
Wisconsin may question this so you may want to file your WI tax return by mail. Attach a copy of your Minnesota return showing that your son reported all his income to MN and write a note explaining what happened. We suggest sending your return by certified mail with proof of delivery.

So I do that even if the W2 says that WI income was $6,261 and his MN income was $53,265.85 which is what matches his federal income?
Yes. If your son never lived or worked in Wisconsin, he owes no WI tax. Your son can ask his employer to issue a corrected W-2 and refund the WI tax. Most employers will not do that. The alternative is to file a $0 income WI return. If you file by mail you will be able to include a statement explaining the situation.
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