Cloudflare's two DNS addresses 1.1.1.1 and 1.0.0.1 have the same hostname, which is "one.one.one.one". That's why it seems queries answered by Cloudflare seem to split into two identical items, infact they are not identical.
This is normal. Cloudflare reports their servers this way, and you are using two separate upstream DNS servers. I have one Pi-Hole with a similar setup as you, and here's what appears in the pihole log:
sudo grep 'one.one' /var/log/pihole.log
Nov 10 01:00:01 dnsmasq[5646]: reply 1.0.0.1 is one.one.one.one
Nov 10 01:00:01 dnsmasq[5646]: reply 1.1.1.1 is one.one.one.one
Then after sudo service pihole-FTL restart and reloading the page, it shows this, and then shortly it will go back to the one.one.one.one.
If you want to change how the servers are labeled, put these lines at the end of the Pi hosts file at /etc/hosts, reboot the Pi. When you reload the admin dashboard, the graph starts out showing 1.1.1.1 and 1.0.0.1, but then correctly shows the local mapping you have put in for those DNS servers.
We had this discussion a few times in the past. It really is a Cloudflare "bug". I contacted their support if this is desired but they never cam back to me (> 1 month ago).