If you are doing free motion quilting, and are getting "dots" of the top thread showing overtop the bottom thread on the back, it's entirely normal and is caused by moving the fabric around and not just stitching in a stationary straight line. This is even more prevalent when the machine itself is moved during machine quilting, and occurs both on the front (dots of bobbin thread ontop) and back of the quilt sandwich (dots of top thread on the back). Longarmers call them "pokies", and PaperPrincess, is correct---it's why it's best to use the same color thread ontop and in the bobbin. Our machines are made to sew in a stationary way. Freemotion and longarm quilting throws a monkey wrench into all that, with the needle flexing in all different directions. It plays havoc with the way the stitches are made, and we just have to accept pokies here and there.