I think it's the composition of my water and/ or stress from the water that makes my koi develop black markings. I remember partially reading about it somewhere but the koi I purchased where chosen for their colors, etc. Then they started having dark coloring on individual scales....sort of like shading part of the scale uniformly throughout the body with lots of black markings on the head. During the seasons you can see changes of more black or less black. More black in winter.
Once when my DD was younger she tried to scrub the black marks off the koi. Didn't work and she got mighty wet
Details of koi when I bought them and how they look here today: photo, top left to right:
Shoji - Orange head white body;
Preggie - red goldie (until about 3 years ago, now white);
Tangy - completely tangerine color koi;
Jackie - red and white shub/wakin (ok);
Quicksilver - completely silver butterfly koi;
Oscar - large scale totally orange koi; and at bottom
Tiger - a very solid colorful & white koi, with
Big Red - red sarrasa. There is also another butterfly koi in bottom photo - Top middle,
Skeletor - who used to be white and now has orangey-yellow and black markings over the white.