I take it you are AD/MIL and the spouse is your civilian spouse. If so, your state of residence is your HOR, which is also shown in box 15 of your W-2. The non-military spouses state of residence can be different from yours and is not all that uncommon either. Depending on what state you were stationed in when married, her HOR could be the same as yours.
Because there are so many possibilities here, it would be more time efficient for you to call the tax advocate at the base legal office to get the clarification required for your specific situation. Base legal has tax advocates on site this time of year. If your AD/MIL, then it won't cost you a penny for reliable information from a tax advocate lawyer that has been specifically trained for the ins and outs of those situations that are unique to military personnel for this particular tax season.