When Sitecore tries to resolve the site for a content item while indexing, it will skip all the non-content sites like coveo_website, coveoanalytics, coveorest, coveoapi, shell, login, admin, service, modules_shell, modules_website, scheduler, system, publisher.
In case if you have a content site which may interfere with site resolving functionality of Coveo, then you can use the attribute called 'mode' in the Site definition. This flag will exclude the site from Coveo site resolving feature.