Irs double dipped

My wife sent a check to pay off her taxes due before I did this years taxes . Then they kept our refund as well for the same . She has called multiple times and gas spent hours on the phone yet they just say they don't show an overpaid account . Kind of funny both checks would create the account to zero . Is there any other ways to go about this . Little upsetting that They are keeping her check and our refund . They make it sound like one of the payments just disappeared.  They also say it could be interest. But that can't be possible  at 80% interst for 1 month payment.  Can you please help.