Residency wrong

You can't change the past. But you can update your W-4 with the employer to be correct from this point forward. But it really doesn't matter (to a degree) because you will be filing a CA state return and an IN state return. The CA return will be a non-resident return most likely. But what you *REALLY* need to do ASAP is get an appointment with the legal office so you can learn if the MSRRA (Military Spouse Residency Relief Act) will exempt you from paying any taxes to CA. As a military spouse, your AD/MIL spouse should have no problem doing this, since it will be free for him. Do note that starting in December the on-base legal office hires temps and spend that month training them for tax needs specific to the military and their families. So don't be surprised when you state your reason for the appointment, if they tell you to "call back next month". That way, they help to ensure you can talk with someone who "really" has a clue.