This happens when a user has been assigned multiple roles. For example a user is administrator, operator and user. In this case the user would receive 3 emails.
This issue is currently under investigation. Even if different roles are assigned to a user, email notifications should only be send just once since this is tied to a user and not a role.
Engineering is currently investigating this and it should be fixed in a future release. There is currently no workaround for this. However, assigning multiple roles to a single user should be discouraged.