This means you've applied too many textures to one quad of a cell. Each cell is devided into quads, and each one of those quads can only have up to 6 different ground textures in them. Black means you've added more than 6. Hit B to toggle cell lines to help see where this may occur (Though it wont show quad lines). You can also put your mouse in the affected area and hit 'I' to see how many textures are in each quad, and what they are. You can select a texture and hit Delete to get rid of it, or right click and say Replace. Remember that replacing/delete a texture will cause there to be a sharp line in the texture at the boundary of the cell, so just check around to make sure things look good, and patch them up.
Once you get used to it, keeping the textures to a max of 6 is pretty easy. I very rarely have to make a tough decision. Only when a LOT meets, like fall forest, pine forest, a road, and a river. Then things get messy and I have to cut textures. But otherwise it's usually fairly easy to do.