What you are seeing is how NY determines part-year resident tax. NY does not tax your NC income, but does pretend that all income is taxable, then calculates what they would tax on that amount, before prorating the tax to the amount of income earned in New York. The way it calculates on the New York return does make it appear that all of the income is being taxed, but it is not. If you look at lines 45 and 46 of New York Form IT-203, you will see the prorate on the NY return.
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