Many states, including California, start from the federal AGI when computing state taxable income and make adjustments (additions and subtractions) based on areas where the law doesn't conform.
Sometimes those adjustments are made to the income, and other times they are made to the tax, after using the full federal AGI to set the tax rate. This is the expected behavior and it is determined by the laws in the states (which vary considerably).
For states that use a different formula to start, there's typically a different number in Box 16 on Form W2 to adjust for the variations in the law.
The 1040 and W2 are used in the state returns where they are required to be, such as in California. California uses the same form for nonresidents as for part-year residents, and all income, whether earned in California or not, is required to be reported and then adjusted.
California first adjusts for areas where the state does not conform with federal law (such as interest on HSAs) and then adjusts for the income earned out of state per California's instructions.
As you work through the state interview for California, the adjustments that are needed will be made so that your home sale will be taxed according to California law - which isn't as simple, unfortunately, as just selecting the income from California and taxing it without regard to other income.
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