That is probably because you uploaded files through ftp, or by using filemanager directly, rather then using the "basic" interface to create one with the help of softaculous for instance.
I can understand that it might be confusing that it says you don't have any websites added. You might be more comfortable by using the link to the top right and switch to cpanel x3 (which is the full cPanel interface rather then the custom that has been a bit simplified).