you should have your employer stop Wi withholding by submitting exemption Form IL-W-5-NR to your employer if you work in Illinois and are a resident of Iowa, Kentucky, Michigan, or Wisconsin.
I don't know if this was the issue but for the correct state credit calculations, you must do the non-resident state(s) first. with $0 tax liability on WI, there would have been no credit computed on IL.
IL and WI have a reciprocal agreement. you only get taxed in IL on wages earned in WI.
so you should have paid tax in IL and gotten back all WI withholding if things had been done correctly
