What your seeing is actually part of the design.
If you look at one of my test sites. 2013.robertdall.com
I am using the monster widget and a couple more widgets and they flow to the bottom of the widget area in the footer. The actually footer is below, you have yours in orange.
But if you have a lot more content then what you have in the widgets you'll see it doesn't sandbox.robertdall.com
That area on the side is actually held for the right sidebar widget area if you take a look at screenshot http://cl.ly/image/2z3c0P312I2T the div outline it shows the below sidebar widget is actually only three columns wide with the fourth column saved for the right sidebar widget are.
You'll have to figure out how to stop those widgets from not entering into the bottom widget area. But it isn't bug.