IL and IA have a reciprocity agreement.  Your Iowa return should only have been filed if there were state of Iowa taxes withheld, and then your Iowa return would show $0 taxable income and get all the money back.

If this is not the case you need to file an Iowa Amended return.

Any wages or salary made by an Illinois resident working in Iowa is taxable only to Illinois and not to Iowa.

An Illinois resident working for wages or salary in Iowa should complete and file the IA 44-016 (pdf) “Employee's Statement of Nonresidence in Iowa” with the employer so that the employer will be aware it is appropriate to withhold Illinois income tax.