I believe the error is regarding the adding of this code in the header
<?php wp_head(); ?> and
<?php wp_footer(); ?> in the footer.
That is a standard thing in theme development and has always been there in our theme.
You can verify that by checking these files.
The problem is, some plugins checker could not pick it up because of how the theme files are structured.
You may ignore the message, the plugin should still as is.