We currently have a O365 hybrid enviroment, additionally we have a transport rule to append a disclaimer for emails comming from outside of the organization. But some emails from some shared mailboxes are being marked as external and the disclaimer is being added to them.
As solution we add them in the exception list from the transport rule, but I'm curious what is causing this to happen.
We are having this same issue. Did you resolve the issue? We are using a relay server for some applications? Also, our MX is outside of O365 tenant.... This has to do with service / auto genterated emails needed for some in house systems. They send/receive TO MANY emails to put them in O365.