This is my exact situation too, but Turbo Tax is telling me I owe IL taxes.

Read my response again. Are your wages your *ONLY* income from IL? If you have *ANY* other income from IL (such as winnings from a casino in one of the many Chicagoland suburbs), the reciprocity agreement doesn't apply and IL will tax your wages.

My only wages from IL is from my Income. Do i still need to file in IL or should I only file WI state taxes?

Same thing. Only made income from IL, and Turbo Tax is saying we owe money to the state of Illinois. However, a CPA we went to said Turbo Tax is doing it wrong.

Same issue with Indiana and Michigan.  Work in MI live in IN, MI employer takes out IN tax only.  TURBO TAX says i need to file MI return.  

@dissconnected Did you earn any other income in Michigan, such as gambling winnings?

Nope. I ended up just not filing the return for MI,as there was nothing for me to enter. I did not owe any city tax in MI as well.

My guess is TurboTax ASKS you to complete a state return for ANY nonresident state where you have income, whether there's a reciprocity agreement or not, and in some cases even if there's no actual income tax to pay (as in Florida, where TurboTax's "state return" IIRC is for a special property tax on nonresident landowners even though FL has no income tax). That's likely because (a) reciprocity agreements are far less common than the usual method of avoiding double taxation (pay nonresident tax then claim a credit for it on your resident state return), (b) reciprocity agreements don't apply to every situation in those states that have them (as I pointed out before), and (c) they don't wanna code individual states' resident/nonresident return rules into the main program. If you know you don't owe tax to the nonresident state, TurboTax apparently allows you to skip it if you insist.