Setup requires more than one user that has the same email address.
One user has access to the issue and one user does not belong to a group that has permission to an issue.
Must have an incoming email handler setup to add comments to an issue via an email reply.
Notification event occurs on issue assignment
Create an issue and assign to user 1 (the one who has permission to the issue)
User 1 receives an email
User 1 replies to the email
Comment not logged because it is interpreted to be associated with user 2

There isn't a requirement that email addresses be unique. May need to either evaluate any user that meets the email address, update the documentation to be clear, or not evaluate permissions.

Minor issue.