I find that, in some GTK3 apps such as Audacious and Evince (Document Viewer), parts of the UI are pure black, which looks ugly and out-of-place. It is not intentional, as the screenshots on both websites show the app looking different. I only have this issue with the Adwaita GTK theme, but since it comes with Gnome 3 and is the main theme these apps are designed for, I'm guessing the problem is not simply the theme having some bug (though the Ubuntu package might).
I have had this issue on two laptops now, running both Ubuntu 12.04 and Xubunu 12.10 with Gnome Shell and Adwaita.
The screenshots below show the problem: Audcious's is visible in the search area around the text box, and behind the playlist tabs, and Evince's is visible in more or less the same position and around the document itself.
Compare this from the Audacious homepage: 
With this image from my system:
And Evince too:
Best Answer
I found the problem - it comes from having overlay scrollbars installed. You can remove them through Synaptic or by entering
EDIT - overlay scrollbars can also be disabled via Unity Tweak Tool. This fixes the GTK3 theme issue without needing to remove the scrollbar package. If you already have removed the scrollbar package, you may need to reinstall it before Unity Tweak Tool will run.