The Waif probably didn't ignore a command to kill someone and instead revenge kill someone totally different. That's why Arya's sight was taken, which eventually led to her having to train blind, which was more of a test of toughness and dedication than intentional blindfold training.
I have less of an issue with that sequence than many it seems. Edmure on the other hand, screw that guy and the way RR went down.
Ahhh, totally forgot she lost her eyes as a punishment. I thought it was more something everyone went through in their training.
Makes more sense.