Why do I have an underpayment penalty for my resid. state of illinois,work in Missouri and overpaid (owe illinois 1400 but Missouri giving me 1200 - refund doesnt count)

Even if I have to pay the difference, I do not understand why Illinois doesn't count the 1200 refunded as me trying to pay enough in taxes to cover them? Not like I can get my company to pay illinois too.....