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Hello,
As you mentioned, it seems that cpanel (WHM) measures bandwidth usage based on domain traffic, and per this cpanel link there are discrepancies. Furthermore, cpanel is an application that runs on the instance itself, measures traffic to some services that are part of the server (through the app per your config), and may not necessarily measure all traffic to the vm instance. That said, you may check for other third party tools that monitors all network traffic to/from the instance as a whole. However, no system is foolproof. Hence, you may contact billing as they are more equipped to help in investigating this issue. I hope that helps.
The billing team will work on your case will involve the technical team (if required) to investigate and verify the issue for which you had been charged this amount. Based on that they take appropriate action.
[1] https://groups.google.com/forum/#!topic/gce-discussion/iCXWCWJb36A