My assumption is that the circuit had an exit node that had (possibly multiple) IPv6-enabled, in addition to it’s IPv4. When the exit node connected to the exit node, it did so over IPv6 since check.torproject.org has IPv6 addresses.
That’s a scary warning to get in Tor browser. Any reason chiwui.torproject.org has an IPv6 address? Can it be disabled to avoid having people (unnecessarily) freaking out over this warning?