How often does it do it? If it is just occasionally, I have "fixed" a few spots by hand. I mark the spot with a safety pin and then later fix it by using a single strand of the same thread on a needle. I go up and down at the same distance as the regular stitching on either sides of the quilt where the long thread is laying. I carefully take a tiny stitch being careful to make it appear that the hand stitch over the laying thread looks just like a regular stitch. I knot and tie the thread and bury the end. It looks just like the rest of the stitching.
Of course this only works if you only have a few spots to fix and would be too much work if it happened every 5 or 6 stitches. If it is happening every 5 or 6 stitches you need to find out what you are doing that causes it. Is it just this quilt? Batiks can cause some quilting problems, so can extra thickness in the seams. I find anything that kind of holds up the timely penetration of the needle can make it miss a stitch. You might try a sharper needle?