Non-resdident State Return

I live and work in MI but my employer is in IN.  They held IN taxes in 2023 but when I did the non-resident return, IN still kept money for the county taxes that was not refunded to me.  They said they were owed for working there, even though I remained in MI for the entire year.  It did not give me an option to leave the county worked in blank and a selection had to be made to continue with the form.  They accidentally held those same taxes for part of 2024 (until I noticed and had it fixed) and I am concerned I will be on the hook for county taxes where I did not work.  How do I ensure my county taxes will be refunded?