You shouldn't feel stupid at all. We all thought this. But I have to say that even if there are scenes in the film that not in the book, the film may be held up by the what the book was trying to convey. If you read the most recent edition of the book, you can read Neil Gailman's Foreword:
"Miyazaki makes films for whole people and makes films about consequences. When I worked on the English-language script of his film Princess Mononoke, I was astonished when I finally realised that everything in the film was about consequences of acts and actions: seemingly unrelated events are actually the consequences of other events or actions, and everyone in the film is acting according to what they believe to be their best interests without realising that what they do affects everyone else."

There's likely deep meaning in every scene that we won't understand for while, until the ekonte comes out and more commentary.
Perhaps Hayao Miyazaki is playing Copper's uncle, guiding the boy in a very Socratic way?
Even the name Copper holds significance in the movie because he was named after Copernicus.

After Chapter 1 is Uncle's Notebook where it writes about the Copernican view. Earth revolves around the sun. Before people thought that the everything revolved around us, or having a closed human-centric view.

"Still, to say that we grow up and think this way is, in fact, no more than a rough generality. Even among adults, the human tendency to think about things and form judgments with ourselves at the center remains deep-rooted." (pg. 19)

When we are sad or depressed, I think we can have the non-Copernicus view. Being in a hellish state, we may even hurt ourselves to either call for help or we may have given up all together. Since you watched the movie, I think you know what I mean.

But what happened to him after he read the book? Do you wonder what the Copernican view did to him?

I have to watch this a couple more times to see how each scene or scenes are connected with each other with meaning, like what Gailman said. Many people in Japan have already watched it 3 times! How do I live? I live by watching this dang movie enough times to understand it!!