not an expert (not even a novice, just a person who taps) in photography, but i think the problem may be the lighting. I can tell color pencil from other colors because of it's some what metallic luster. The color pencils which are water soluble don't have it, but the oil based ones have it. Usually fix that stuff, you would want to add diffused lighting and removing directional lights, and maybe have longer exposure period in a lower light environment
Is it not more likely the screen you're viewing on more than the scan itself? By default, screens (with colour mixed from light) tend not to accurately show anything scanned/photographed correctly (with colour made from mixing pigment).
[Edit] P.S. your tone, shading and colour mixing in this picture is exemplary