Most of them are probably skipped because they are binary files that do not contain code that could be executed on your server (like images and compressed files). Some may also be empty file and are skipped because they cannot contain malicious code if they contain no code at all 
You should be able to click on the skipped files count and then hover over the files on that list to display the reason.
You can also change the comma separated list of file extensions that are skipped but that would only slow down the scan process with no better results.
