I don't think she's done anything wrong, certainly not in terms of her confidence - that's great. But I think that when you come into a new culture - which she has, a subculture in fact as the Royals are a really weird when you consider it culture all of their own - you are going to ask questions and not necessarily accept things exactly as they are. And perhaps that's led Harry to think 'You know what? This is a bit bonkers, I want to do more, and why do I have to ask my big brother anyway?' and start shaking things up a bit. And that in turn has rattled some cages, and caused friction.
Ultimately if there's a fault here I'm not sure it lies with a person so much as with the fact that monarchy as a concept is very much out of step with the modern world and the concept of meritocracy, and it's bound to cause friction when you raise people to be in the spotlight and to do things but then also tell them they can't be too much in the spotlight or change anything, but must also be a 'breath of fresh air'. Something there has to give - it's just a question of what, and when.