When using TurboTax, after completing your federal tax return, then prepare a VA non-resident return requesting a refund of all taxes. Finallly prepare a MD resident return. Alternately, the easiest way would be for you to paper file the VA763S form: http://www.tax.virginia.gov/sites/tax.virginia.gov/files/taxforms/income-tax/2016/763s-2016.pdf as soon as possible to get your money back.
Expect to pay a MD late payment penalty as you did not address this issue earlier in the year. For 2017, file form VA-4 to stop the VA withholding and begin making quarterly MD estimated income tax payments.
See: https://ttlc.intuit.com/questions/2895760-which-states-have-reciprocal-agreements
