So it looks like you did the same thing every year, putting your payroll deduction amount as a contribution outside of your employer.
I hate to say this but if you did, you may need to amend the returns for 2013, 2014, and 2015, to remove that deduction. It's a bit difficult to predict the result, because it will depend on whether or not you had excess contributions and withdrew them, or let the excess carry over to the next year causing a 6% excise tax, but to prepare you, you may owe tax for each year.
As for Missouri, did you do Illinois first? In most cases (naturally, there are exceptions), you do the non-resident state first so that its tax can carry to your resident state. I know that Illinois tax gets deducted in Missouri (I did it earlier this year, although I don't remember the exact details), so make another pass and see if it works...
