I have the same issue with tor 0.4.8.9 in Whonix (sys-whonix in Qubes OS).
I think the same issue is reported here:
Using Tor Browser in whonix-workstation-17 based qube or using Firefox in debian-12 based qube connected to sys-whonix I can use onion sites without an issue but clearnet sites are starting to break after some time after sys-whonix startup.
Downgrading the tor packages in whonix-gateway-17 template fixes the issue:
sudo aptitude install tor=0.4.7.16-1 tor-geoipdb=0.4.7.16-1
If I use Tor Browser 13.0.5 with integrated tor 0.4.8.9 inside debian-12 based qube connected to clearnet then clearnet sites work without an issue so this problem is probably related to Whonix.
I can also see these messages in sys-whonix tor log when trying to connect to clearnet sites over sys-whonix:
[warn] Not attempting connection to [scrubbed]:80 because the network would reject it. Are you trying to send Tor traffic over Tor? This traffic can be harmful to the Tor network. If you really need it, try using a bridge as a workaround.
Maybe there’s a problem with sys-whonix configuration.