It doesn't make sense that your IL income should say a different amount from your Missouri income on your W-2, given the circumstances that you describe.
If you are a resident of Illinois, your home state will tax you on all of your income, no matter where you earned it. The procedure is to prepare your non-resident state return first (MO) then prepare your resident state return (IL), which will give you a credit for the taxes paid to MO.
However, it doesn't make a difference what box 16 says for Illinois on your W-2. Your resident state is still going to tax you on all of your income.