From reading the background information in your question, I can understand your concern about possibly being  double charged, but I do not have enough information to provide a definitive answer.  For one thing, I am unfamiliar with the contractor's standard accounting procedures and practices such as how they classify, group and accumulate their indirect costs including what costs are included in the fringe rate.  I recommend contacting your cognizant DCMA office to see if they have any information about this company's accounting practices and rates.  DCMA hopefully can help you find out (if they don't already know) what costs are included in their fringe, and they probably would be able to review their fully burdened labor rate to determine if it's structured properly.  Another option is to contact your Region's DOL Labor Advisor who can verify the rates are from the most current wage determination and may even be able advise if the contractor has applied the fringe and H&W correctly in their labor rate.