The extra space comes from the diagonal bits, i.e. the incompletely filled squares. The slope of the diagonal line is higher to begin with in the bottom picture, which would have the effect of raising the total area beneath the "curve" so to speak, if it were not offset (which it is) by that hole. Makes perfect sense if you look at it for awhile and think about it.
Edit:
Another way to think about it. Forget about puzzle pieces and just think of a diagonal line sloping up from an origin. In this case, each picture has just 2 line segments that make the diagonal. If you were to calculate the area beneath the two you would find the bottom picture would have more area. This is because its higher sloped segment comes before its lower sloped segment. * Thus to make the area equal some space has to be removed from the bottom picture. It just so happens they thought of a clever puzzle piece arrangement to make this scenario happen.
* To see this even clearer, imagine a horizontal line and a vertical line. Arrangement 1 has the horizontal first, then the vertical, and as such has zero area under the curve. Arrangement 2 has the vertical first and the horizontal second and has a large area under the curve.