So I’ve been having this problem that I’m sure many other people have where basically if I use the extrusion tool and extrude to the same place, it creates dimensionless faces that I can’t find out how to delete. If you go into face selection mode, they appear on the edges of the area you extruded. This also sometimes happens at random, without using the extrude tool. I’ve tried googling this but found no results. Hopefully someone already knows a solution to this problem.
Select all verts affected and W / remove doubles. Look in the toolshelf or F6 to adjust the Merge Distance if required. At the top of the blender window it will tell you how many vertices have been removed.