Mirai's program looked nearly clean (as did her program at Skate America), but then the scores come out and she's marked below Alaine C.'s two-footed program and Anna P., with her hand down on several jumps. Both of those programs looked really messy. And she was robbed on PCS at COR, at least. Why are under-rotations penalized so much more than a rotated jump with a step-out, hand-down, two-foot or even a fall? I think if a skater can't hold onto a jump it should get only 70% credit (at most) with a mandatory -2 (at least) GOE. The system is so inconsistent--alternatively nit-picky on things that can't be seen with the naked eye and lenient with things that can be -- that it just kills enjoyment for most spectators. And only a very few skaters can live up to the demands of the IJS on a consistent basis--right now, there are none.
The difference between a jump that is UR and a jump that is rotated but sloppy is that the UR jump starts out with a lower value than a fully rotated jump, but also that by definition it cannot get positive GOE. The judges can take off GOE points for sloppy execution, but they aren't allowed to add GOE points for a UR jump, no matter how good it looks to the casual viewer.
There are few skaters who can get through a FS without URing at least one jump, but most of the top elite skaters fully rotate most of their jumps. If a skater URs one jump, it won't have that much impact on the final score, but Mirai URd 3 jumps, two in combination, and got a downgrade on a fourth. That meant the values of those jumps were all reduced to begin with, and then got negative GOE as well.
By my calculations, if Mirai had rotated all those jumps and received + GOE for them, her TES would have been 66.11 instead of 52.60, and her PCS score would have gone up considerably as well. She would likely have won the competition handily.
The problem is her basic jumping technique is what causes the URs, and at her age it will be almost impossible to correct.
The crowd at CoR reacted well to skaters who fully played up their performances, like Jason Brown and Misha Ge, and of course to their own skaters. Mirai's deadpan performance was well received at Skate America, but the CoR crowd expected a more emotional Madame Butterfly and they were unmoved; the judges had to have felt that, hence the lower PCS scores.