Hello and welcome to PSG.
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.
Hopefully someone else will have a better answer.