I'm not getting the CoverFlow interface partially appearing in windows like you are, but on two of my Macs, I've noticed hundreds of +error: unknown error code: invalid drawable+ messages in the console from Safari.
I think it's definitely a problem with CoverFlow, as when I launch Safari without going near the History or TopSites screens, I don't get these messages. As soon as I invoke the History window (CoverFlow view), once I return to browsing, the messages start. It's something to do with Safari capturing and caching screen images.
The way I've avoided this until it's fixed is to change my default homepage to anything other than TopSites, and to use the History menu rather than the CoverFlow view.
I've certainly had a few little glitches in Safari 5.x generally.