I am also experiencing this issue since updating to v6.
The pihole.log file shows a response from my router as an 'NXDOMAIN' when, for example, trying to access my Home Assistant server. This was working in the seconds before updating to v6 with no other changes made to my router or network setup.
Feb 19 17:50:24 dnsmasq[2141273]: query[A] hass.domain.home from 10.0.0.39
Feb 19 17:50:24 dnsmasq[2141273]: forwarded hass.domain.home to 10.0.0.1
Feb 19 17:50:24 dnsmasq[2141273]: reply hass.domain.home is NXDOMAIN
(my domain replaced with 'domain.home' for privacy)
Please upload a debug log and post just the token URL that is generated after the log is uploaded by running the following command from the Pi-hole host terminal:
Note that these are using .local TLD, which is reserved for mDNS protocol usage and should not be mixed with plain DNS.
You should remove/rename those entries.
Since you state that resolving hass.domain.home has been working previously by virtue of Conditional Forwarding retrieving names from your router:
Would you router perhaps know other names, and does it support reverse lookups to get a name for an IP, e.g. dig -x 10.0.0.1 @10.0.0.1 for your router's own name?
I also notice that your Pi-hole has processed a request from 10.0.50.97
*** [ DIAGNOSING ]: Pi-hole log
-rw-r----- 1 pihole pihole 8.4M Feb 19 21:39 /var/log/pihole/pihole.log
-----head of pihole.log------
Feb 19 00:00:12 dnsmasq[1734551]: query[A] time.nist.gov from 10.0.50.97
As your router's subnet is 10.0.0.0/24 , that's an IP outside of your router's subnet.
Do you perhaps have another router in your network, managing 10.0.50.0/24 and associated names?