Best way to get things fixed, send a message via the contact us on their web site, state facts of the agreement and what is been billed wrong, give them a reasonable date to have it rectified by (say by the next billing cycle) and tell them if it's not you will be going to the TDR to sort it. And here is the important bit, if they fail to sort it out actually follow thru with the TDR, It seems VF are quite well motivated by the TDR to sort things out.
Been there done that with the original issue a year ago which was unreliable data metering, causing excessive costs to some customers, and their refusal to rectify the metering system until TDR came involved.
This problem is much easier being billing but its interesting that the billing is regularly wrong.
One thing which seems consistent is that whenever there is any financial error, its in the favour of the supplier
As a guy who works on identifying and trying to fix the financial errors not in VF's favor I can assure this is not the case. You just don't get a lot of customers complaining about it. I do once recall a phone call I took as a CSR back in 2007 where a customer complained about an error in their favor. I don't think they really clicked it was in their favor despite attempts to explain it. I fixed it and they were happy with the revised invoice.