I think one aspect of the novel that you are left with is the uncertainty of the future life of Hannah Tupper. We know that she is moved to a safer location upriver, but one wonders if the persecution that she suffered will spread or if she will be allowed to live out the remainder of her years in peace.
In addition to post #2, my students were fascinated about the practice of marrying girls off and them having no say in the matter. The restrictions on the young people, especially girls, raised quite a few eyebrows and questions about why they didn't just refuse to comply. Seeing the restrictions and social customs of the past makes students today feel thankful that they didn't live in those times.
I am not sure if you are asking about specific questions within the novel, or if you are speaking of questions the novel raises for the reader. The novel "The Witch of Blackbird Pond," is a wonderful tale about Kit, a 16-year-old girl who was raised by her grandfather on the island of Barbados. When he dies she sells everything to pay off his debts and escapes marriage to an older man by sailing to Connecticut. In the village of Westbrook Kit moves in with her aunt, uncle, and their two daughters.
Some of the questions raised in the novel are centered around the independence of the colonies from England. Kit wonders how her uncle can be disloyal to King James. We wonder what will become of the colonies. At one point druing a meeting with the new Governor the lights go out and the Charter for the Colony disappears. The question arrises as to what happened to that Charter? Who took the Charter?
There are also questions about Kit's involvement with the Quaker, widow Tupper. Was Hannah Tupper a witch? Did she teach Kit how to be a witch? Is Kit guilty of casting spells. Many questions were raised in the trial of Kit.
Hope this helps answer your question.