Yes I've seen the same thing in ebony and rosewoods. really stands out in some rosewoods. Maybe It's a result of the tree trying to heal Itself, I'm not really sure. It can also happen around pin holes that may be from some kind of wood eating insect, but point is I have seen what Eric mentioned.
We all strive to make the cleanest looking cue possible, but unfortunately not every cue comes out perfect, and at least for me, playability & solid construction are the most important things. I think a lot of us would be less then honest if we didn't admit to at least trying a marker or dyes to touch up a cue, so I can appreciate Sherm's honesty. Much like Him I once tried a marker to touch up a cue, and had the same results. No matter what I tried, It was obvious, and I was very dissatisfied with the results. Same as him I cut It out. Luckily I was able to do that because I tested It before final size. I think the result would have been worse then the original imperfection anyhow.
One thing I've noticed about a marker being used is often the spot can have a sort of purplish tint to It. Not all markers are pitch black, therefore It can stand out even in ebony.