This response is based on the information provided.  We suggest you discuss with your contracting team, program manager and/or legal department as appropriate.

It is not an unauthorized commitment.  The work was properly authorized with use of an appropriate contract action.  Additionally were3 this an unauthorized commitment, the contractor would have to determine whether to process a ratification; a ratification definitely does not apply in this situation.  The contractor simply needs to refund the overpayment to the U.S. Treasury as you have identified.