I'm guessing it's because it's the short program and they did not complete the requirement. For example, in Sr. ladies the combo must be a double-triple, triple-double or triple triple. Mirai's single toe did not meet the requirement. Similarly, there must be a double or triple axel. This penalizes those that do not do the required elements rather than just taking the lesser single axel score.
I'd have to check the tech notifications, but I'm pretty sure that's why.