If an instance of Sakai uses an external User Provider (e.g. institutional LDAP directory) then users who are joined to sites will no longer appear in "Site Info" if their external record is deleted (e.g. they leave the institution).
The logs show messages:
org.sakaiproject.site.util.SiteParticipantHelper - SiteParticipantHelper.prepareParticipants: user not defined <userid>
Now because they don't appear in Site Info, it is not possible to clean up these "de-registered" users, so this situation cannot be resolved easily without doing some work at the db level.