I just found its a known issue and theres a quick easy fix for this.
go to Settings>All Settings>Miscellaneous>misc.dnsmasq_lines and add this text in between the quotes "no-0x20-encode" and save
And be sure the custom server says 127.0.0.1#5053 like it says in DoH instructions
Source:
You can verify its working by going to 1.1.1.1 — One of the Internet’s Fastest, Privacy-First DNS Resolver it will tell you if DoH is working