If California tax has been withheld from your military pay, then yes, you want to file a California return. As is shown at the following California FTB website: CA Military Income, a California resident stationed outside of California is not taxed on Military Pay, because California no longer considers it to be "California Sourced".
Make sure your W-2 is marked as "active-duty" pay, and carefully follow the prompts in the California State return to mark that you were stationed outside of California. If you do that, your Military Income should be excluded from California, and, since CA tax was withheld on that income, you should receive a refund of the withholdings.
Contact DFAS to have them stop withholding CA tax from your Military pay if you do not wish to go through this every year you are stationed outside of CA.
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