I have had the exact same thing happen with flannel, and it was a good quality flannel - Woolies by Bonnie Sullivan, from Maywood Studios. I honestly think it's the flannel and not the seam allowances or thread or anything you did.
I'm wondering if the dyes they use have anything to do with it. The first quilt I ever made was a flannel quilt, can't remember what brand of flannel, but that one is wearing thin everywhere, not just the seams.