If a domain is mapped and it has no extension (eg: http://mycompany ) then you cannot delete the mapped domain. The only way to remove it is to delete the whole site it is mapped to. This is a bug.
The issue is related to the WHMCS Provisioning plugin which is what caused this problem to surface. Member of staff entered into the domain field what they assumed would be the sub-sites sub-domain/directory location but this is not the case when creating an order from the admin side, even though the Domain field is populated with the sub-directory AFTER the site is created.
Main issue right now is that you should be able to delete anything that is entered into the mapped domain field.