This is a known issue with Cloudflare. Cloudflare also needs to issue SSL certificates for your domain to secure the connection between your visitors and Cloudflare, and other to verify your domain name, they will publish their own hidden records on the _acme-challenge subdomain, which takes precedence over your CNAME record.
The only thing we can do on our end is to check for this. But we cannot fix it, as this is a Cloudflare restriction.
If you are going to use Cloudflare, you don’t really need a regular SSL certificate anyways. A self signed SSL certificate works just as well, given that Cloudflare is handling the SSL that your visitors actually see.