Did you enter all of your NY withholding? Go back to the federal section and make sure you entered all of your withholding. And make sure you have entered NY for any state withholding. It is very easy to enter NJ or NM when allocating withholding to a state. You have to go back to the source documents (w2 or 1099).
Did you make estimated payments to NY? If so, those are entered on the federal side also; see link.
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