Who hasn't questioned the actions of a Rav, even though we know him to be a Tzaddik? That takes a tremendous level of emunah, pure faith in God, and even when we do overcome these doubts with our unshakeable faith, who could deny these thoughts didn't at least try to surface?
Rebbe Nachman explains (Likkutei Moharan II:52) that it is perfectly natural to have questions with Tzaddikim and not to understand them or their behavior. This shouldn't bother you at all.
Why? A Tzaddik is forever trying to liken himself to HaShem, and HaShem's actions (let alone His thoughts and plans) are beyond our reckoning. So, we will always have questions on HaShem, which means in turn, we will always have questions on the Tzaddikim who are constantly emulating Him.
[Curiosity: This is another good example of how Hassidut anticipates and answers post-modernism.]