Hi…
You can manually checking on html page source to verify if css/js minifying works perfectly, see if the files called individually or minified. You can also use firefox to inspect element or firebug to check it.
The reason for the problem because w3tc using php on wp-content.
About warning error, mostly it just a warning, but this problem with wp-content hardening was real can be easily verified like above. I’m no longer using Sucuri as i harden it manually, I don’t know if this issue solved or not by current release.