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I assume you were taking this on Schedule A, Miscellaneous. The program believes you are aware of the laws relating to the entry of items in that area. e.g. Investment fees for a shelter investment account are not deductible, but for a taxable account they are.
If you believe the taxpayer met all of the requirements for these grad school expenses to meet the NYS requirements, then write a protest letter to the assessment.
The program is only a tool, not an auditor.