New York non-resident and part-year resident returns can be confusing. New York uses 100% of income to calculate tax as if all of it is New York income. They then calculate the percentage of that amount that is New York income and that is tax. The issue could also be that you haven't properly allocated your income in the New York tax section of the program. It starts out as if all income is New York, and then you have to allocate it accordingly. You may want to revisit the New York state return section of the program.
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