Long story short: There is a good chance your fingerboard was dyed black. After dressing it, some of that wood would have been removed and you are seeing where the dye penetrated deeper into the wood. Whether or not it has been dyed, often there are deposits in the wood that look like these little bubbles. They can also be covered up by making the fingerboard darker.
I could be wrong, and encourage our luthier friends to chime in, but here's my two cents on what I think is happening, from what I've seen with ebony frogs.
Most ebony isn't as black as players want it to be. Especially with a piece long/thick enough to make a bass fingerboard, there are going to be some imperfections in it. Lighter streaks of greys and browns are very common and unless they're the result of knots in the wood or some other structural problem, the colour differences are normal and do not change how the wood performs. I personally think it looks great "raw" and that the colours add "character" but most players don't feel that way, and think it indicates inferior wood. Since there is nothing wrong with the wood but a lot of players are skeptical, a lot of shops/makers use dyes to darken the wood and keep players happy.
This is not "Ebonized" wood, or pulling the wool over the customers' eyes. Yes the wood is being dyed darker. It is still ebony, not someone trying to pass off Maple or something cheaper as Ebony (which you see on cheaper basses that have painted fingerboards) but it's the same as putting a darker finish on an instrument. Poplar is popular for backs and sides now, but the wood can occasionally have some nasty looking greens and greys in it. With a dark finish, it looks fantastic, but "in the white" it might not.
What can you do about it? You can live with it, as there is nothing "wrong" with it other than aesthetics. Or, you can talk to a shop/maker about it, and see if they would re-dye your board. Some makers/shops don't dye their boards and will not be willing/able to do this for you. If they do, depending on the process they use, (this is already more trade secrets than the Illuminati would like disclosed) it could be more expensive than you want it to be. It takes time and bench space, has to dry, and sometimes they have to repeat the process more than once to achieve the colour/look they are going for.
If you are otherwise happy with the setup/work of that shop, talk to them and see if they'll do it for you.