Yes, sometimes the order the states are done in TurboTax matters. If you did the Illinois first, it might have picked up the Wisconsin tax erroneously.
Yes, you want zero income allocated to Wisconsin but you also do not want a "credit for taxes paid to another state" on your Illinois return.
To be safe, I suggest you delete the Illinois return, do the Wisconsin non-resident return first. Allocate zero to Wisconsin. You should get all the state tax refunded. Next do the Illinois return. You'll be charged Illinois tax on all your income.
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