That is happening because you enabled virtual hosts. Unfortunately, that's the only way if you want to use OwnCloud with other applications.
My recommendation is that you create a set of domains or subdomains, with A or CNAME DNS records pointing to your server.
After that, update the domain for your virtual hosts, in the case of OwnCloud you can do so in the following way:
If you have any other virtual host, apart from the default one defined for LAMP stack, you must modify the
ServerName (holding the main domain, e.g. yourwebsite.com) and
ServerAlias lines (e.g. www.yourwebsite.com).
After modifying the files, a restart of Apache should be enough:
sudo INSTALLDIR/ctlscript.sh restart apache