WordPress W3 Total Cache Plugin not combining CSS & JS
I use manual disk minify. In my situation w3 total combined JavaScript and CSS. Therefore I recommended to use manual minify (disk). Then go to w3 total minify tab and click on the top "Help" button and add all the necessary js and CSS.
Once added js and/or css remove if there's any queries strings (add js and css direct link) eg:- wp-content/theme/mytheme/style.css
This could break your site. Therefore add js and css step by step.