Hmmm, hard to tell for sure by the picture but it looks to me like you may have had transfer of the marking tool to your thread and the coloring is embedded in the fibers of your thread. To tell for sure is to take out some of the quilting and see if the mark is still on the fabric or there is actually color residue from the pencil in your thread. I had that happen to me once and nothing got it out until I ripped out all the quilting. Then the marks were gone because they were in the thread, not the fabric and I requilted.