The cells are the areas closest to the voronoi sites, the dots inside the cells. The sites are the outputs of the optimizer; it adjusts the sites until the constraints are met well. The number of sites is chosen by the user.

The excess sites will naturally be clustered together and weakly tend away from the interior walls. The optimizer prefers straighter walls, so it tries to cover the room in large cells (which have big straight edges) and then shove the rest of the points into a small area where they aren't affecting the internal walls. Thats why they tend to cluster into the center of internal rooms, or towards exterior corners where the wall is preset.