When you prepare your state returns, prepare your Indiana PY return first and then your Illinois return. When you prepare your Indiana return, pay particular attention to how to allocate/separate your Indiana income so you will be taxed only on your Indiana income.  if you do this, then Illinois return should be correct based off of the information you place in your Indiana return.

Hello, I completed the Indiana PY first, however, the IL wages are flowing from my W2 and aren't being reduced by the wages from Indiana.

To a naked eye, it appears that all your income is being taxed in Illinois.  That is not the case however. if you look at your Illinois IL-1040, it starts out with the Federal taxable income and continues with this same total to line 9. Then it gives you an exemption amount in line 10. Line 11 should accurately reflect what portion of your Illinois income minus the personal exemption amount for the year.

if you viewed this in the Illinois tax Summary in your Turbo Tax online return, then you would actually need to view your Illinois IL-1040 return to see how the taxable amount was determined. Of course, you won't be able to see this unless you pay for your Turbo Tax product first.  One of the drawbacks for using Turbo Tax Online but otherwise, it is a great product.