The image you provided shows that the two dark lines are different colors and were created on different layers.
Line 1 is darker and on a layer above the lighter colored line 2.
Notice the pixels at the edge of line 1. They're lighter at the edges (aliasing).
Since line 2 is beneath line 1, you can't see the lighter pixels but they are still there.
Even though the layers have been merged, the lighter pixels show up after you make the selection and copy it to it's own layer. As to why I'm not exactly certain. It's been explained to me that it's the way Photoshop averages pixels within the selection, but I don't know if this is accurate.
I don't have a good answer as to how to solve the problem at the moment but I can say that repairing the faded/transparent pixels would be easy. Just re-select the line (2) and use the Brush Tool to fill in the missing pixels.
There may be an easier fix but I would need the original file to examine. There are many variables that are outstanding that I may not be aware of.
Sure, I can see the result as much as the next person but whats wrong with it?
Ctrl + J duplicates the pixels on the selected layer onto a new layer.
If you were copying and pasting those pixels then sure, there may be some issues with copying merged layers or such but a 1:1 duplication is just that....a duplicate.
There is nothing wrong with the duplication, its the pixels on that layer that you have an issue with....and who created those pixels?
There is no 'solution' as such as nothing is wrong.....its how you've created the pixels on that layer that's the problem.
I agree with Sam that the image suggests more than one layer.....maybe you deleted something on the uppermost layer which also took out the underlying pixels too?
Its impossible to say how this happened but its an easy fix.....you can copy the pixels higher up the line and paste them into the hole.....just be aware of transparency though....overlapping transparency will always get darker....you may want to clean up the hole first or paste to a new layer and delete / mask what you don't want.
I've just realised that when you say 'solve' it that this could mean "Yeah, I know its wrong and I know why but how do I patch up those pixels on that layer?"
If that's the case then ignore the path I was following.....use the 'Clone Stamp' tool, or copy / paste...whatever method you want to 'patch' up the hole....but like I said, beware of transparency.
You could of course just copy merged the initial marquee and paste to a new layer instead of duplicating the layer....depends what you want to copy really.