We're talking about when one side is sewn down one way and later the same seam allowance is sewn down another way, right? I used to let them go all whichever way but lately I've gotten a lot better about managing my seams and only have a couple flips per quilt - recently I decided to quilt a top I finished a couple years ago and the 'hither and thither' way the seams were laying drove me a little bit crazy when I tried to press it all out. I didn't use to press my quilt tops before quilting either, which is probably why the flipped seams were never on my radar.
But now I do press my tops, and I don't clip seams or re-sew when I find flips; I just press it down the way it's sewn at the start, open it about halfway between the split and press that part open, then let the flip have its way for the last bit. That way I'm sort of "easing" into the flip and it's not as noticeable on the front if it's all flipped in the same spot.