I experienced the same bug too but that bar would go away after I reboot.
Did you try entering killall Dock in the terminal,
It tells the dock to restart. It normally gets rid of those glitches.
I had that problem using the Developer Preview, now on 10.9 Release it's working fine, but other report that too, I guess a fix will come out before long.
No thanks, there are applications that I don't wish to close.
The killall Dock command restarts the dock but doesn't close any applications.
The easiest way to fix it is to drag off downloads from the dock. Then from Finder, put it right back. Problem solved.