Just watched on Universal Sports. IMO the judging seems correct. Just because Miki was "clean" doesn't mean she should be miles ahead of Yuna, because that assumes everything else is equal, and it's not. For example, Yuna's layback looked to have four features, so it should have gotten level 4. Miki's layback had one feature (8 revs in one position) so it should have gotten level 1, and my guess is it also got minus GOEs. Then Miki's PCS were probably affected because she stood there for an eternity before the steps -- obviously that layback was supposed to have more features (sideways-leaning spin was one she attempted but didn't hold for the required 3 revs since it was badly centered from the start), but she exited early and the music had to catch up.
Miki skated great, for sure, and deserves to be 1st, but Yuna's basic skating -- her posture, especially -- is so much better. JMHO.