I hate when this happens so here is what I do. When I'm setting my seams before pressing them to one side, if there is a seam where the seam allowance is pointing the wrong way on the bottom side, I put a tiny spot of Elmers school glue just at that spot. When you then press the seam to one side, that little sucker is glued down and will not give you a problem when you sew over it. The glue washes out, the frustration is gone and it's quicker that re-sewing any twisted seams. I usually repair seams when I do them twisted and it bugs me every time so this way cuts my stress level!