There is no documentation for dnsmasq warnings, hence, I wrote descriptions for every possible warnings I found in the source code. The documentation can clearly be improved as we see these warnings in the wild. A session is one minute by default, so what you are seeing doesn't look like a bug.
Actually, it is quite interesting that you see this only once per two hours (or whatever, but notably less than every minute). I tested quite a few servers and haven't seen such warnings a single time. The lack of reports on our support platforms suggests it is something special to your network.
What router and internet access do you use? Could you imagine anything that would cause this to happen?
Hypothesis: Your ISP is may be manipulating certain queries your Pi-hole is doing only once every two hours (TTL of 7200 seconds). Somehow this manipulation makes the DNS packets too big leading to truncation, triggering this warning.
You can get rid of the warning by adding a config file like /etc/dnsmasq.d/99-edns.conf and adding
edns-packet-max=1280
in there. Then run pihole restartdns and your Pi-hole will not even try with larger packet sizes (our default is 4096).