$72 sounds like the federal PPR fee, if a state return was filed, that would be a separate fee.

The only time Ive seen it charge twice for the same return is if you deleted it and them recreated it or (created a separate file in addition to the one you used for the extension and youre trying to use that separate file as the actual return) or you changed the EIN after the first time you paid.

You can view your PPR audit report to see what you were charged for.   Tools > PPR > View Report.   

If you were in fact charged  twice for the same exact return, they will refund your money if you call support.