I've only made one quilt and didn't have that problem but I did have some strips that didn't line up properly so I appliqued a patch over that area. Since it was a baby quilt and the original panel had some butterflies on it, I decided that the extra butterflies needed to fly away into the border area. Just covered those misaligned seams right up. This would surely cover up your frays but not sure if it would prevent your seams from further fraying during future washes.