It is a little unclear whether you are working for the military or a private company. Your employer's claim (if it is a private company) doesn't make sense. If you are "exempt" then you should have a salary normally. You should try to talk to someone else at HR if possible to clarify. If you feel that you are not being paid properly, you can hire a private attorney (I handle wage claims) or you could contact the labor commissioner of California (just type in Division of Labor Standards and Enforcement into Google).
More information, including your contract and your exact job title, and the relevant work, employer and documents may need to be reviewed to render legal advice. This is general informational advice, and may not reflect your situation. This does not create an attorney client relationship.