Sometimes I sew the seam going one way, but when I go to sew the other end, it needs to flip if I messed up my sewing order. So I intentionally twist the seam allowance in the middle of the block instead of at the intersection so that there is not so much bulk at the intersection when I go to quilt it.
If it is a case where the machine feed dogs twist the seam, I undo it just a little ways and fix it.