You’ll have to investigate your theme’s files, likely in the functions.php file there will be a script function that should be using wp_enqueue_script. If it’s just outputting the scripts incorrectly then it won’t be using wp_enqueue_script.
However, it could also be other plugins, if you’re running plugins that put scripts in the header. Again, you’ll have to hunt through the code or contact the theme developer.
It’s likely that somewhere scripts are being printed directly into the wp_head hook instead of using wp_enqueue_script. Could be your theme (in functions.php or a page template file like front-page.php or home.php) or in a plugin.
I’m going to close this since I haven’t heard back, feel free to follow up if you have any other issues.
