CA does have an exception that allows a separate CA return even if filing a joint federal return. If one spouse is CA nonresident all year and does not have CA source income then the CA resident can file a separate CA return. Here is CA reference. The CA resident spouse would follow the same procedure as the MA resident spouse. Create a "Mock" separate federal return with only their own income/deductions and print/mail the separate CA return.
If you do not fall under the exception and must file a joint CA return be sure to indicate in the federal "My Info" section and the CA residency questions that your spouse was CA nonresident. This will allow you to allocate the non-CA source income (spouse's MA income) out of CA to eliminate the double taxation. If filing a joint CA return using the joint federal return the TurboTax will attach all necessary forms in the e-file. Typically, unless you are claiming a credit for taxes paid to another state you would not need the other state return sent to CA.
The MA separate return will use the federal AGI from the "Mock" federal separate return. MA requires a separate return when the spouses have different residences/residency periods.
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