It sounds like you haven't allocated your income properly to Calif. Here's how it works in TT/Calif:
The Calif nonresident/part-year return, Form 540NR, computes your income and tax as if you were a resident the entire year, then computes a net tax rate by dividing the total tax by total taxable income. Your California-source taxable income is then multiplied by that net tax rate to determine your California tax. You can see this on Form 540NR lines 31-37.
So you do report everything but towards the end of the interview (Nonresident Adjustments) is where you allocate the California-source income which is multiplied by the net tax rate. See Form 540NR, lines 31 - 42 and Schedule CA(540NR). So for each federal income item on the left, be sure to enter only the Calif-source portion of that total: 1) all received while living in Calif, plus 2) income from a Calif-source (rental property there; property gain/loss located there; etc) while a nonresident, etc. If none, enter 0.
