This just happened to us too. I used TurboTax which auto-populated my state return and apparently incorrectly put MY wages in the credits column, causing a big difference in adjusted income between federal and state returns. As I had not paid the extra $ for the CPA protection that year I am apparently stuck with the large bill we just got from CA FTB, even though the error was caused by TurboTax. After 9 years using them to do my taxes I will be going back to doing them via an in-person accountant from now on as I feel I can no longer trust them to carry forward my federal inputs to the state return.
