Robert Newton Peck's novel A Day No Pigs Would Die is semi-autobiographical, and the protagonist is modeled after himself. There are at least two good reasons why these "misunderstandings" add humor to the story.
First, there is a need for levity (humor) in this novel because the major events of the story, though sometimes lighthearted, are fairly serious. There are several life-and-death incidents, culminating in his father's (Haven Peck's) death. Even small misunderstandings help lighten the mood of the story.
Second, a young and generally innocent narrator is going to make mistakes in understanding which are seen as humorous by a more mature and experienced readership. (A classic example of this is Scout in To Kill a Mockingbird.) In this case, Robert has lived a fairly sheltered life, and it is through his "misunderstandings" that we realize key truths of the novel.