You should probably be aware that Docker is IPv4 only by default, so seeing network unreachable messages for IPv6 upstreams would be expected. Also, such messages aren't critical, as long as your container is still aware of an IPv4 upstream.
Picking IPv6 addresses as Pi-hole's upstream DNS servers doesn't make much sense in such a configuration - just stick with IPv4 and untick IPv6 upstreams.
Note that for getting Docker to work with IPv6, you'd need to enable IPv6 support in both the container you want to use IPv6 as well as the Docker daemon itself.
In addition, the latter would currently only support IPv6 with Docker daemons running on Linux hosts.