It usually refers to the email notification from MyCIC with the subject "Your application (EXXXXXXX) has been updated"
There was a time a few months ago when the system seemed to be buggy and people got these emails for no obvious reason, hence them being called as "ghost emails".
These days, I honestly think the system isn't as buggy as it used to be, as receiving this email now does correspond to changes to one's profile, like if the applicant edited their Express Entry profile, or a CIC employee changing the progress status of a visa application on the back-end.
(I can't believe I answered this question, LOL.)