Phantom Faces and Normals I have a mesh that had some trouble spots where I had extruded faces into the mesh and It left some extra faces that caused dark spots when I rendered it.

I've gone through and deleted all the faces but the dark spots are still there and when I show faces normals the direction indicator is there but no face to delete.
Removing doubles will merge vertices that are close together, in your case you still have duplicate vertices that are further apart than remove duplicates is configured to merge.

You can increase the merge distance used by pressing F6 or looking at the bottom of the toolbar region.



You may also want to switch to vertex select mode to see where the extra vertices are and either delete them manually or move them closer so that remove doubles works, snapping can be used to move them to the same location for merging.