There's also artistic intent. Some people will look at a character design and think "the darker skin is an extremely bold color so it doesn't look as good with their costume color scheme" or "a lot of this issue is set in poor lighting with deep shadows. I should make the skin a bit lighter so they don't fade into the background as much," without stoping to think of the racial issues that come along with this.
Who knows why certain colorists pick the shades they do, even on no racial issues. Pick up some random issues of Wolverine and his hair will be anything from mostly black, to gray, to blue looking.