Some requests are not reaching fly.io servers

is your SSH/TLS settings on Cloudflare set to Full?
As for the output regarding Cloudflare proxying:

  1. Delete the DNS record to your app on Cloudflare
  2. Remove fly certs: fly certs remove example.com
  3. Recreate app cert: fly certs add example.com
  4. Add DNS record on CF: Type: CNAME, Name: @ for root or w/e for subdomain, target: your-app.fly.dev IMPORTANT: make sure you disable proxy, it should read DNS only.
  5. Wait a few minutes then go to your site. Once the TLS connection is good, you can switch to Proxy

You don’t need to setup the acme challenge