[rudra]

Actually, why you should use Lets encrypt while you already have Cloudflare SSL?

And, try to turn off Cloudflare DNS then do lets encrypt once again. If you turn Cloudflare DNS on, then the lets encrypt is trying to contact with Cloudflare's DNS.

thats kinda mixed up.

DNS and SSL are not the same. As I'm sure you all know. One can use Cloudflare DNS with either Letsencrypt ssl or cloudflare ssl. Just dont use both.
Actually you can use both too. You can configure that way and then cloudflare backend will talk to your server using letsencrypt ssl cert over https instead of plain http and you viewers will see cloudflare ssl cert on your site.

@Rehan

I updated. check my post above now.

The reason may also be a faulty plugin or .htaccess . But we will go there if the above solutions dont work.

let us know.