Your active duty pay should be subtracted from your IL tax return so if you had no other income you should not owe tax.  Make sure that you indicated that you were Active Duty in the Personal Info section, then go back to Illinois income and it will ask "Any Military Pay?" then you can enter your active duty pay. 

I did this. I don't know what I'm missing, unless TurboTax assumes I'm my wife, but under Income under State it says Military Pay Adjustment and says the right amount. I don't know why I'm owing to IL

Did you wife have income (if she is IL resident too)?

She had income in KS only. On Turbo Tax I put her resident state as KS since she lived and worked in KS all 2017. is that right?

If she was an IL resident when you got married, she would be eligible for MSRRA which allows her income to be taxed in IL only but not if she had KS taxed withheld.  Otherwise, is her income being taxed in IL?

She was, but she had ks tax withheld. I don't think hers is being taxed in IL. We put KS for all her information. How do I check?

Illinois is taxing her income as well.  You will want to file Kansas as a nonresident then she will get the withholding back and then you can use it to pay the IL tax.  If she qualifies as IL resident, you want to keep it or she will have to stay as KS resident if you PCS.  She can also ask her employer for the form so that KS tax is not taken out so you do not have to file two returns next year.

Illinois requires you to file Married Joint state if you did for federal and treats both spouses as residents even if one is not.

Okay but we already got our KS and Federal returns back. Will this affect anything?

Illinois got rejected.

You will have to amend the Kansas return and just change residency to nonresident.  Did it say why it got rejected?

Yeah at first I put nonresident for Illinois and it got sent back with 4 different codes and now that I put full time resident it now says I owe.

Yes, you will owe as resident.

I went to change it and it says my wife and I are both nonresidents for KS.