Mirai, unfortunately, has a history of under-rotating her jumps—especially the all-important triple-triple combo. Though she’s been working to address it in recent seasons (with mixed results?), once you get a reputation for that with the judges/technical specialists calling the elements, you’re almost automatically under additional scrutiny about it. Ashley Wagner has dealt with this as well (see her results in Sochi for instance), but not to the same degree; and the judges generally helped her more in the PCS than they do with Mirai.
And, surely part of the score difference is the backloading of Zagitova and Medvedeva’s programs. Plus, they don’t seem to be subject to the same level of under-rotation scrutiny and edge calls that other top skaters in their field are—this complaint of mine is mostly applicable to Medvedeva.