Look at the screen captures. I sent the blend file to play with. SO, I selected the area that has a mesh under the top mesh which happened when using Modifier Decimate after using Subdivision Surface to remove unnecessary quads. I noticed the double mesh in the face in Solid view when I was finished Decimating and selected the vertexes using wireframe. Next I selected Mesh / Cleanup /Merge by Distance. Upon sliding the Merge by Distance to the right, these marks start appearing. I used the same file again and repeated the process to see what would happen if I continued dragging right and the screen capture shows the result.

Pushing on with the example, this is obviously the wrong way to try to rectify the "under mesh" situation as I will never be able to put eyes on my horse with this still messed up mesh. But I am curious about this occurrence nonetheless. I looked at it in Shading view and it looks alright although there may be some flipped faces to fix as well. I will go to a much earlier version before using Decimate and try something else. I wish Decimate worked to somehow detect and reconnect/remove parallel "under" meshes as it is being used. Maybe this will be a future enhancement.

Apparently using mirroring to try and add eyes to the face does bad things? Unfortunately I'm not sure if I had Mirroring ON when using Decimate--if that complicated things -- I think not. However the effect is very direct when switching it ON and OFF as shown in the screen captures. It looks like the problem is caused when using mirroring as it attempts to mirror using an already existing mesh -- maybe a beginner's mistake, but then how can one make changes later to add more detail using Extrude? I'm thinking that because Sculpt has Mirroring built in that the assumption is that it would be used for this situation.....

Hi Ankit,
Thanks for the interest. At this point I'm not sure this needs more attention. The more I read about using AMD's GPU with Blender the more I'm coming to the conclusion that it is not fully compatible. This is an excellent case.
I continued to work with this mesh and ignored the colored edges since they didn't affect the look of the Shading. Eventually I found the Add-on, Mesh: 3D Print Toolbox. One of the choices actually selected all of the SUB-meshes in my entire mesh and corrected it with Make Manifold -- a miracle!
I am just hanging in and muddling through the learning process" by doing" even knowing that without a CUDA compliant / imitating GPU that things are not going to act "normal". I will endeavor to find "errors" and report them but this one I would suggest is just a GPU anomaly that can be ignored but now "known".
Paul

Some clarification:

• colored edges are edges marked "sharp", see https://docs.blender.org/manual/en/dev/modeling/meshes/editing/edge/edge_data.html#mark-sharp-clear-sharp (there is nothing really wrong with that)
• you can turn them OFF here

• now you have a combination of Custom Split Normals and smooth shading, which will indeed cause Merge By Distance to add these sharp edges (this wasnt always the case, I assume it started with rB93c8955a722b: Mesh Edit: preserve Custom Normal vectors in topology operators.)

Here is a much simpler file to check:

I will now check if this change is intentional, not sure yet...

Thanks you Philipp for showing how to turn off the green edges, but I am curious about why they were marked initially. I can't see anything "sharp" about them as they are on a flat mesh, not on a steep edge. I turned them off an ran Mesh Analysis in Wireframe and there are lots of other "errors" colored but none of those green edges. I then ran 3D Print add-on and Check All. It showed 7 Sharp Edges but none of the green and exactly as expected on tight angles. The marked green edges seem to be specious and perhaps an artifact of having done a Vertex Merge by Distance? Yes, averaging instead of marking seems a better option -- marking green is just worrying and doesn't seem relevant.

Here is an example of case where attempting to preserve custom normals by generating shapr edges makes sense imho (once you have merged the mesh back into some sort of cube, compare shading whit what you get if you remove sharp edges).

Think this should be an option. Also, this is missing from the modifier equivalent (weld)...