We do make an attempt to capture these. Chances are you have a client which is not defining various headers.
Are you able to grab the headers from such a reply and to provide more information on the client? Perhaps you could open an issue with this information?
When we send messages from Moodle, we add certain headers to tell clients and MTAs not to reply because it's an automated message (see them at https://github.com/moodle/moodle/blob/master/mod/forum/lib.php#L744). When we receive messages back, we have a look for certain headers which common clients set in an attempt to ignore them (see those at https://github.com/moodle/moodle/blob/master/admin/tool/messageinbound/classes/manager.php#L751).
Unfortunately there is no fixed standard for either the outbound or the inbound headers. We've catered to all of the cases we could find, but clients which are going off the beaten path will cause issues. We can address them on an individual basis, but there is no perfect cure short of a standard being perfectly implemented by all MTAs and clients...