A bit unclear as to how you filed. Here's is what "should" have been done.
1. Completed federal return.
2. Completed a PA part year return reporting ALL income earned while a resident of PA , regardless of where earned. The program gives you opportunities to adjust the amount of income to be taxed by PA.
3. Completed a VA part year return only being taxed on income earned while a resident of VA.
So you should have received a partial refund from PA. As other have mentioned, if the VA employer withheld PA taxes while you were a VA resident, that is the source of the problem. It's unclear when she obtained the VA job but her paperwork must have shown her as a PA resident. You need to get her paper work corrected and a letter of explanation to PA along with some proof of her living in VA is in order.
