smart uv unwrap creates duplicate (not overlapping) uv mesh segments I scan a bust of someone and get an xxx.obj file and a texture file. The mesh is too dense and also needs repair so I make a separate obj file to repair. During the repair it loses the texture. 
I bring in the original mesh and the new mesh, align them (ether in meshlab or visually in Blender). I remove duplicates in both meshes. Then I unwrap the new mesh using smart UV unwrap. Then I bake the original texture to the new mesh.

Besides finding overlapping UV meshes (fixable), the issue is that there are more than one UV face for certain areas. I get duplicate individual faces and duplicate multi-face areas in the uv map. 
The resulting model has bits of the shirt color in the face and vice-versa. 

When I select the troubled faces in the editor view, multiple separate areas in the UV image map light up. When I paint the face, the shirt gets bits of the skin color, etc. I can't seem to delete the bad duplicate faces in the UV mesh.

Is this a problem with Blender 2.72 or am I doing something wrong - and how to I fix this?

Thanks for your help.
B

UPDATE: I've uploaded a blend file at  . I've created  completely black testuv.png file an as soon as you open the blend file, you'll see the mesh and the UV editor panel.
Notice that two faces are selected on the mesh edit panel and on the left two completely separate pairs of UV faces are highlighted.  This occurs many times after doing an unwrap using Smart UV Project..
Notice that I painted the face area red and see how many red triangles there are in other parts of the mesh.
I do see areas of overlapping mesh but I can fix those manually. I can't seem to separate the duplicate UV meshes or delete them.
You can re-do the unwrap and recreate the problem.
Thanks.
These are not not duplicate face they are vertices shared between these faces and are highlighted on both of them and that's because you are using vertex select mode if you switch to face select it will be clear





something to note about UV mapping :

each vertex has a general index obj.data.vertices[index] and loop indecies (one or more ) obj.data.loops[loop_index] which is used in the UV mapping so each vertex can have more than one UV coordinates in the UV map. UV coordinates are obj.data.uv_layers[UVmap_index].data[loop_index] 

in a nutshell when UV mapping you are dealing with faces not vertices



UPADATE: 
The problem is with UV unwrapping which is producing scattered face from different regions  and the low resolution texture image you are painting on ,after using texture paint on the face only :

 

you can see that the paint spreads to different regions and that's because of :


UV unwrapping ( small spacing , and scattered faces ) 
Texture low resolution (compared to the mesh density )




what you can do is :


unwrap again with larger margin
use higher resolution texture


OR:


try another unwrapping method


Note : 


you may want get ride of the extra vertices using Remove Doubles ,
you can paint texture directly on the mesh with Texture paint mode