The organization has many team sites and sub-sites that are not listed in the Site Collections part of the SharePoint Admin menu. Have the sites been created incorrectly? I have tried to search for the sites that are not present, and Search doesn't find them that way either.
In Admin center, we can only see the Site collections list but Sub-Sites are part of Site collection and live within that site collection.
you will see only site collections, but when you click any of the site collection url and get the properties of that site collections then you will see the number of subsites in that site collection.
Sub-Sites are not site collections.
They wont be listed there since they are only a "site"
Anything directly under /sites/ is a site collection. Also the root sites, search and the mysitehost are Sitecollection.
A Sitecollection can have a quota assigned and is not inheriting security from its parent (Its a security boundary) , since it has none.