Hello,
What version and license of phpdocx are you using? If you are using a purchased license please send to contact[at]phpdocx.com the email or username of the user that purchased the license.
phpdocx doesn't remove contents using the CreateDocxFromTemplate class unless specific methods to remove elements are called. The content of some fields (such as fldSimple tags), for example page numberings, are handled by MS Word and other DOCX readers automatically.
Regards.