Preventing PHP and other malicious code

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I had a fresh install and added this plugin pronto and configured all the options to the most secure settings. I also have the config file moved up to prevent hacking.

6 hours after creating the now WP install I get a notice that I have 383 codes added to the site files after SPECIFICALLY telling it not to allow malicious codes including .php, .pub, .txt.

It only seems to be good at notifications and not prevention.