Much of the ebony used these days isn't not pure black ebony.
Some if not most is dyed black.
What you may be seeing is the grain.
If so, there is nothing wrong with it.
Now on a different note,
I use finger board oil on the fret boards, on all my guitars.
Be sure to use the proper oil.
Check with your manufacture to find out what they reccomend for your guitar.
http://www.zzounds.com/item--ROCRTFO