Apparently, there's are many JS that cannot be minified. But if you're using W3Tcache, then you could solve this by manually selecting the files to be minfied and those to do not minify.
1) go to Performance>General settings> [tick: enable; manua] and leave deafults
2) save all settings
3) go to Performance>Minify>
4) click [empty cache] ;
5) click [help] >> here you will see a list of suggested stuff;
-Google ads (or any ads for that matter)
-Any stats.wordpress.js files (you will have these if you have jetpack installed
However for CSS you can pretty safely select all of them. Now this isn’t an exact science as this is minifying your theme files (Don’t worry it’s non destructive) and there are alot of different themes all employing a wide range of different files, plugins and functions. Like my theme file cannot be minified because i'm using a child-theme (that use @import).
So (expect from other your basical settings):
And in the css list do not put http://www.yourwebsite.com/wp-content/plugins/flare/css/flare.css?ver=1.2.4
6) Basically preview your changes before submitting them.
Minify is one of the biggest improvements you will be integrating, once you have selected all your files (and done the same with every theme, if you are using more than one) then click “Apply & close”, directly followed by “Save all settings” (Deploy it if your site still looks/works the same).
Hope you can solve it.. ask me if you have some issues!