There are a number of different problems that are part of the plot in Wednesday Wars, and as I am not sure which one you are referring to, I will address two that I believe are the most pertinent. First of all, at the beginning of the book, the central character Holling thinks that his teacher, Mrs. Baker, is out to get him. In the situation from which the title is derived, Mrs. Baker is stuck with Holling alone on Wednesday afternoons when the rest of the children attend religious education classes at the Catholic Church or the Jewish Synagogue. Holling thinks that Mrs. Baker resents this, and is plotting his demise. This problem is solved as, through her kindness to him and her challenge to him to really think about things that are important in life, as inspired by the writings of Shakespeare, Holling begins to grow in maturity. He develops the ability to see things from other perspectives besides his own, and comes to see Mrs. Baker as an exceptionally caring and strong individual who is deeply concerned with his well-being.
Another problem in the book is Holling's relationship with his father. Holling's father is controlling and unloving, and demands unqualified obedience to his wishes without consideration of what his children, or his wife, for that matter, want in any given situation. He is single-mindedly focused on getting ahead in his business, and plans for Holling to follow in his footsteps. As his awareness of his own identity in the world develops, however, Holling discovers that what his father wants is not necessarily what he wants, and he fears that he will never get the chance to determine his destiny. Happily, Holling discovers the strength, through the support and affirmation of Mrs. Baker and others in his school community, to stand up to his father, and take control of the direction his own life will take. Holling's sense of self develops to the point that he is able to extend the love and support he has received to others who need it; in particular, he finds a kinship with his sister, who is similarly repressed by their father's domineering ways. The author communicates the sense that both Holling and his sister Heather will rise above their father's shallow value system and heartless control and become fully realized human beings.