For reference, I am filing federal taxes, nonresident state taxes to IL (where I work) and full-time resident state taxes to MO (where I live).
At the end of my taxes submission, on the Tax Return Alerts page, it says:
Double-Check Credit Claimed for Taxes Paid to Another State
For the Credit for Taxes Paid to Another State claimed on your Missouri return, you entered the same amount of tax for the other state as your tax withheld by that other state. Your tax amount for a state is usually not the same as your tax withheld by that state. Your other state tax usually is the actual amount of tax shown on that state's tax return.
If you're filing your other state return with us, we recommend that you continue and get a preview copy of that state's return (NOT the Missouri return). Make sure you've completed your other state's tax return. Look on the other state's return and find the line showing the other state's tax. Then go back to the Your Taxes Paid to Another State screen and change the other state's tax amount to the actual tax on the other state return that was from income taxed by both states.
There is a second box that pops up, stating:
Update Taxes Paid to Another State
Listed below are your income taxes you told us were paid to other states. If you've made any changes on your other state returns, you should make sure the amounts below are correct.
IL: $XXXX
If you need to change any of these amounts, please go back to the Your Taxes Paid to Another State screen.
So on my Nonresident return, I said I paid the above amount. I am not quite sure what the issue is.
Thanks for any help or support!