Unfortunately no one here can see your CA tax return, but it must be showing some CA taxable income. I would suggest reviewing the CA Form 540NR line by line to see if you can find the error. If her CA 540NR shows zero CA taxable income (line 35), she should receive a full refund of her withheld CA taxes.
**Answers are correct to the best of my ability but do not constitute tax or legal advice.
