You potentially created a partial "DNS forwarding loop" if enabled CF and have the Pi-hole IP configured in the router as the WAN DNS.
Some queries might get trapped bouncing between router and Pi-hole causing high number of queries, high load on router or Pi-hole and maybe even time-outs.
A trapped query looping looks like this:
Client --> router --> Pi-hole ---
^ |
| |
--------[CF]-------
When have Pi-hole configured in the WAN DNS settings of the router (which is doing DHCP), you dont need CF.