Well that might be because you have already pointed the domain to CloudFlare, so it is resolving to that IP, you would have to do this when your IP is not registered to CloudFlare and then link to CloudFlare after the registration of lets encypt.
That’s just a guess, I did mine when it was linked to CloudFlare so I am unsure.
Edit: I did some looking up and DigitalOcean confirmed in their own tutorial that you would need to disable CloudFlare temporarily in order for it to work, that’s obviously just for the registration, after which Let’s Encypt will know what IP to resolve to.
“Note: If your domain is routing through a DNS service like CloudFlare, you will need to temporarily disable it until you have obtained the certificate.”