I doubt if these are all genuine bugs but they are irritants:
At the end of a kernel update, using Entropy, the option of automerge in equo conf update for /etc/conf.d/modules doesn't "merge" the files, just replaces the existing "modules" with a new one so it's necessary to edit it again for things like vboxdrv.
The hostname issue was driving me crazy but that appears to have been addressed.
I'm using KDE 4.2.1 on a fully updated system and can never be sure that my sound is going to work properly. There tends to be a notification that my HDA intel (ALC888 Analog) isn't working so the system is falling back to PulseAudio but if I select PulseAudio as the preferred device very little works in the way of sound. I could go on about sound issues in KDE 4.2.1 but am assuming that it's one of the irritants of using a very new GUI.
The biggest bug of all is me! (failing to notice things properly)