Hello,
The native conversion plugin supports a set of contents and styles when transforming DOCX to PDF detailed on https://www.phpdocx.com/documentation/conversion-plugin/preparing-the-templates-for-its-conversion (Supported OOXML tags and attributes when using the native method section).
It seems your template uses some not supported content or style. From the warning you get, maybe some numbering style or format not supported. For this reason a PHP warning appears; also please note that it's not a PHP error, so the conversion shouldn't stop.
If the DOCX includes contents or styles not supported by the native conversion plugin when being transformed to PDF, we recommend you use the conversion plugin based on LibreOffice (https://www.phpdocx.com/documentation/conversion-plugin/information).
If you send to contact[at]phpdocx.com a DOCX sample you are transforming we'll check and send it to the dev team. Each new version of phpdocx supports new contents and styles in the native conversion plugin.
Regards.