This is normal, minification of CSS/HTML and JS is not a magic button. If you have no plugins and 1 style-sheet and minimal javascript (aka not more than 1 function) it will work, but anything above that and your looking at conflict and load order problems.
To properly minify takes work, you have to either do it manually or figure out what is causing the conflict and fix it, in many cases it’s simply not worth the trouble.