Illinois Form NR

The letter you received should tell you the specific items on your return that the state disputes.

If you disagree with their findings, the letter should contain instructions on how you can appeal.

If you decide to appeal, pay attention to any deadline dates for making the appeal.

if the w-2 showed X$ of Illinois wages that's what Illinois will go by.  if it includes wages that you believe should not be reported to Illinois you need 

Line 5: Wages, salaries, tips, etc.
Enter the amount shown as Illinois wages on the Illinois copy of the
W-2 forms you received while you were a nonresident.
Do not include any Illinois wages you received while
you were a resident of Iowa, Kentucky, Michigan, or Wisconsin.
you were living in Illinois only to accompany your military
service member spouse who was stationed in Illinois.
you were living in Illinois and elected to use your military service
member spouse’s state of residence for tax purposes.
If the Illinois wages as shown on your W-2 are incorrect, you
must attach a letter from your employer, on company letterhead,
stating the the correct amount of Illinois wages and the number of
work days performed in each state. If any of the compensation was
earned in a prior tax year, (i.e. deferred compensation or exercised
stock options), the statement must include a detailed calculation of
how this income has been sourced. We will not accept a letter from
you or your tax preparer.

column B of form NR should only be pulling in the Illinois wages as entered on the W-2.