He didn't like everything about the film. He was vocal about how the ending completely contradicts his message: "Paul was a man playing god, not a god who could make it rain." In fact according to a later book making it rain would >!doom the entire spice trade!<. So maybe the sonic gun was another aspect he wasn't a fan of.

I had a hard time trying to visualize what was going on at times, especially the moments when they'd drop into the matrix. And I'm still confused about the ending. It was my first cyberpunk novel, and only one so far, so maybe I just need more experience with the genre.