I looked at the protocols, and I really don't have a problem with the scores as they are. Yuna's base values are 28.5 to Miki's 28.7. A stepout on a jump is supposed to get -2 to -3, which converts to a -1.4 to -2.1. However, judges are supposed to start with the positive GOE first, then do the subtractions to end with the final GOE. Yuna's 3lutz was fully rotated and more massive than ever before the stepout (maybe its size was the reason she stepped out). The judges still gave her more than -2 on the element, resulting in a -1.5 point loss. Her PCS deserves to be higher than Miki. And when you put it all together, she's in first by a hair. It's completely consistent with the rules.