One of the biggest reasons that your SSL won't generate properly is due to you pointing your DNS records incorrectly. Whether that's having the wrong hostname or having the wrong content/destination IP to our server, or even forgetting to set up the "www" hostname "A Record". All of these can cause your SSL to not generate.
For steps on how to properly set up your DNS records for your website to our servers please visit this article for non-Cloudflare users DNS Setup Using Cloudfalre or DNS Setup for non-Cloudflare users.