She must file both. The employer should have been withholding NJ taxes only, unless she worked in Philadelphia.
If you are a New Jersey resident and your employer withheld Pennsylvania income tax from wages, you must file a Pennsylvania non-resident return to get a refund. To stop the withholding of Pennsylvania income tax, complete Form REV-419EX, Employee’s Nonwithholding Application Certificate, and give it to the employer.
She will then have to file a NJ resident return. She might be assessed underpayment interest and penalties there.
