Flight crews and other employees engaged in interstate transportation are subject to special rules of taxation. Her employer can tell her what percentage of her flight time is in each State.  

The pay of an employee who has regularly assigned duties on an aircraft in at least two states (e.g. a pilot or flight attendant) is subject to income taxation by his or her state of residence and any state in which the employee earns more than 50% of the pay received [49 U.S.C.S. §14503(b)(2).  An air carrier employee is deemed to have earned more than 50% of his or her pay in a given state if the flight time worked by that employee within that state exceeds 50% of the total flight time worked by that employee while employed during the calendar year.

An individual may be able to claim a credit for any taxes paid to another state, when over 50% of pay is earned in another state.

If she has withholding from the State of California she should file a California return, to recover any refund due to her.