After you went through the California interview regarding residency, when you went back and saw the YES answers, it was a default selection- as you go through TurboTax makes the changes based on your entries, but the interface you see will always go back to the default. (If you were to continue without making changes, TurboTax would update to the selection on screen.)
Because you will use Part-Year status separate from your spouse for Virginia, you are correct that your Virginia income will be taxed by Virginia but not taxed by California so the credit for taxes paid to another state will not apply.
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