Without being able to see her return, it would be very difficult for us to say.
How about you/she go through Form 1-NR/PY and check each line that appears to be an income item? It might be easier to work backwards, start with line 25 (Taxable income). If it's not zero, keep going up the form to see why it's not zero, and then come back to us if you have a specific question.
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