Ibibo Group / Goibibo — Charges unauthorized extra amount.

I paid online booking from goibibo and at the time of check-in hotelier asked me for extra amount. He said that he has my booking details but didn't got my payment which I paid online.
I called up goibibo customer care several times to get my issue resolve. But even after waiting for 1.5 hours at the hotel lobby, my issue wasn't resolved. Later I paid the difference amount of Rs.388.44/- to the hotelier and then he allowed me for check-in.
I need the amount refund which I paid to hotelier. Even after mailing all the details a month ago, this issue is pertaining and company didn't helped me out.