Actually both Mirai and Rachael got a UR call (Mirai on her 3lutz, Rachael on the 3toe after her 2axel). Mirai may have lost a tiny bit more points on her UR due to it being on a higher scored jump after the halfway mark, but really it's a wash. The difference in their FS score (not their total score!) is 7.15. From studying the protocols, here's where Mirai really lost to Rachael:
Obviously getting 0 points on a spin element hurt. She normally gets 3.5 points+ on her flying sit spin.
In terms of points they got from jumps, Rachael got 3.37 more points than Mirai on them. They actually made very similar mistakes on their jumps. They both got UR calls, they both doubled a planned triple, and had a wonky landing on their final jump. So why the point difference? Because Rachael had a jump plan that scored more points to begin with, so with them losing almost identical points with the failures thrown in, Rachael came out ahead. Summary of Rachael's superior jump plan:
Rachael's two (planned) repeated triples were 3lutz and 3flip, whereas Mirai planned to repeat her 3lutz and 3toe.
Rachael put her highest scoring jumping passes in the second half, whereas Mirai had one of her highest scoring jumping passes in the first.
Rachael planned a 3sal (for a 7 triple program if she landed all her jumps) whereas Mirai planned a second 2axel.
It's almost uncanny that they wound up losing identical amounts of points from their planned jumps. But since Rachael had more points to begin with, she comes out ahead.
Mirai also lost around 3.5 points for getting a big fat 0 on her flying sit spin.
The remaining point or so difference in their FS is in the PCS, where besides skating skills, Mirai came out slightly behind in all other areas (and fairly so, given how tense she looked whereas Rachael actually took time to perform and sell the program).
And there you have it. That's exactly why Mirai lost the FS to Rachael and the whole competition.