Can a medical facility refuse to bill Medicare as a Secondary Ins.?

My primary insurance made a payment on services rendered to me,I have Medicare as my Secondary Ins the payment made by the primary was very small because the facility was not in network the check was sent in the guarantor's name it was deposited and a personal check was sent with a copy of the explanation of benefits from the primary carrier to be submitted to Medicare for balance billing the facility posted the payment as a patient payment and not an Ins payment,now they refuses to bill Mcr using different excuses now I am being told that they cannot bill Mcr because the facility is not in network with my primary ins,they want to send the bill to collection,I have been a biller for hospitals for over 25 years and have never heard of such a thing.Can someone help me solve this problem.