when ever i use flannel (or any heavier than cotton fabric) i adjust my pattern and use 1/2" seams. one way to make sure you have the top and bottom even for piecing you should have the bottom fabric show just a thread or two beyond the top piece that way when you sew you know the back is caught in the seam just as well as the top. also, prewash flannels. thin, loose weave, single sided flannels fray the most, if possible always try to find the thicker double sided flannels. but i think if you make sure your fabrics are evenly together and you use a wider seam you will not have this problem anymore.