You have to file a Louisiana tax return since you have income from there. Your spouse does not under military rules.
You can claim Indiana as your resident state since it is your spouse's state of record. So, you would normally file as married-joint on your federal and your Indiana returns and as married-separate in Louisiana, just for you.
You could also file as married-separate federal and state as you have been doing. You should choose which method works best for you.
Indiana will be your resident state under whichever method you choose, so you should look for a credit for taxes paid to another state when you prepare your Indiana tax return.
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