Hi Em,
have this also from time to time (via Qubes Updater). Did you check, if the updater (at least) did some of the updates? In the result section I always have 1 of 2 failed (Debian) messages and 3 of 6 failed (Fedora) messages. In such cases I always run the Qubes Updater a second time so it often will update the previous failed ones too… Orange star is gone then.
Earlier (in my qubes life) I also always did manual updates, but I didn’t do this in the meantime any more. Always try to solve such with the qubes updater - even if I have to restart the machine/or restart the whonix-gw (my updater qube) between updates to get them finally solved…
Yes, it could be really a pain in the arse, but I pressure myself to get it finally working with the qubes updater, than the manual update.