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A PA resident is not taxed on their W-2 income in MD and visa versa. If the W-2 lists MD withholding the program will not understand and you will have to file for a refund in MD showing it all to be taxable in PA. You do this by starting with the Information Worksheet and reporting a nonresident state and overriding the amount to be taxed in MD. If however there is income from anything other than W-2 wages then there is tax in MD as the reciprocity only applies to wage income.
If your employer is withholding taxes from the state you are working in, and you live in a reciprocal state you need to have employer correct W2 so it doesn't happen next year. There is no need to override anything in the program, as you just file a non resident return for the state that taxes were withheld from, and a resident return for where you live. At the bottom of the federal worksheet part X1 is the info for nonresident tax info.
Yes it is from a W-2 and the software calculates tax for MD. There is withholding for the special nonresident tax and that is correct but I am also getting income tax. I could just not file a MD return. Let them ask for it later as no tax is due. .