When adding a new domain in cPanel (for example: newdomain.com), under additional domains, automatically creates a subdomain with the login of the new domain (Subdomain username / FTP) + main domain (for example it will look like this: newdomain.maindomain.com), you cannot delete or cancel its creation.

What would prohibit indexing and browsing of the site through a subdomain, you need to do the following

In the directory of additional domain newdomain.com (this will also be the directory for your subdomain: newdomain.maindomain.com), in .htaccess add the following lines:

RewriteEngine On  
RewriteBase /  
RewriteCond %{HTTP_HOST} ^newdomain.maindomain.com  
RewriteRule (.*) http://newdomain.com/$1 [R=301,L]  

This will perform a permanent redirect to the new domain. After a while search engines will "forget" about newdomain.maindomain.com, because getting 301 ([R=301,L]) code implies "permanent redirect".

Code 302 ([R=302,L]), indicates a temporary move and used, for example, that would redirect users from all pages (otherwise it reindexes the page when there is no information) to a certain site, which indicates that conducted temporary work on the site or in other similar cases. Then search engines will not "forget" about the existing addresses in the database.