SmarterMail does not have any logging indicating the user had marked an item as Not Spam. This would only effect the system if bayesian filtering is used in your environment.
Since the delivery session shows it completed, and was not marked as spam it's hard to say how the items was actually moved into the Junk mail folder.
Does this user happen to use Outlook synced up via IMAP ? Outlook will move items to the junk mail filter if this functionality is enabled within their Outlook profile.
Technical Support Supervisor