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I think you're being lied to by whomever sold you the car.
If the check has been paid there is no way USAA can stop payment on it as it can't go back in time. It can request the funds from the recipient's bank but if they're not there they can't get them.
USAA should know if the check was paid.
I have no idea why a bank would say a check from USAA is fraudulent. I have no idea why the seller wouldn't return the check to you.
I'm not sure that USAA can be responsible if you bought a car from a crook. Don't give him the title until you get the check.