I'm late to this party, but to everyone wondering why Shahai wasn't given clear orders: my take is that in Daiyu's mind, his orders were clear: teach the Seppun. But Shahai thought she saw some subtext that said, "Don't teach the Seppun". Hence her internal conflict.
Shahai comes across as someone who doesn't intuitively understand other people very well. She tries to make up for this by analyzing everybody, but that leads her to second-guess everyone's motivations, causing strife and misunderstandings with her siblings. It seems entirely in character that she'd misread her father, as well.
Unfortunately, Daiyu isn't likely to clarify his orders because he doesn't realize they've been misunderstood, and Shahai isn't so stupid as to send a letter asking, "Hey, should I actually obey the Emperor or not?"