I was active duty and my spouse was charged for state taxes from two different states, how can I fix this?

I was active duty military for most of 2016 and stationed in NC until I got out in December. My wife and I are both from IN which is where we just moved back to. She has worked all year in NC and then in Indiana in just the month of December. After going over her W2 and paystubs I realized she was taxed for both NC and Indiana. I know that she should only be paying Indiana taxes under the Military Spouse Residency Relief Act (MSRRA), so how can I get her W2 fixed or file our taxes correctly?