If the scratches did occur when sharpening the cause would have been from not holding the blade properly when using the sharpmaker. Or you were taking metal off the shoulder of the edge rather than the cutting edge. IIRC Spyderco uses a 20 (40 all together) degree angle on their knives.
If you're using the knife, I'm assuming you are because you sharpened it, then you shouldn't be too concerned about scratches because it's going to get a lot more from use.