If you separated in September and New York was your Home of Record, you would have to file a PART YEAR return for New York and a PART YEAR return for Virginia because you were a New York resident while you were still in the military. New York is subtracting your active duty pay because you have the nonresident return and military pay is only taxed in the resident state.
If this is not your situation, please clarify and add any other questions in the comments.