1. NY allows the student loan deduction for residents against their total income. Nonresidents are not entitled to the deduction since only the nonresident income is being taxed. See IT-203-I (Instructions)
2. Review your entries and select the NYC nonresident, did not work there, not needed. One of those must be caught in the system trying to get the city return added. You may need to go through those questions and then logout. Clear cache and cookies and try again.