It depends on the configuration you have set in the plugin. If you’re using the free version then only files in the <head> section are combined. Files in the <body> and inline-scripts are ignored. You would need to use settings Deluxe and higher (only available in the Pro version) to combine all the files on the page.
…Also files that are loaded from other codes/files cannot be optimized by the plugin since they are not embedded in the HTML. It’s better to view the source of the page to see what is excluded than use the results of a performance tool.
Hi and thanks for your plugin. I have a similar issue. The plugin doesn’t combine /wp-includes/js/wp-embed.min.js and /wp-includes/js/wp-emoji-release.min.js. Are they inside the body or it’s an issue of the plugin? I am using WP 4.5