if its a wall hanging- no one is going to know unless you point it out- so many of our (boo-boo's) are simply never noticed by anyone else unless we make a point in showing/telling about them- if you don't mention it-anyone looking at your quilt will believe it is exactly how you planned it to be- no one knows different unless you make a big deal of it. and since there are no 'quilt police' i don't know what you are worried about-
as far as the marker goes- if your white stitching bugs you & you want to cover it- go ahead- it's yours to do with as you please.