It's not flagging "bad" things, as such. The theme check is designed to be a non-perfect way to test for compliance with the <a href="https://make.wordpress.org/themes/handbook/review/">Theme Review</a> guidelines. Not all themes must adhere to these guidelines. The purpose of the checking tool is to ensure that themes uploaded to the central <a href="http://wordpress.org/themes/">WordPress.org theme repository</a> meet the latest standards of WordPress themes and will work on a wide variety of sites.