I try to always be careful with my pressing and matching seams, etc. but these flipped seams seem to occur somewhere in each project. I am able to quite cheerfully live with it and have had no other problems from them. I do press them extra well to get them as flat as possible and make sure it's not visible from the top side. After that, I count them good as and move on.
I'm glad I have a nature that lets me do this.