In your SUMMARY.md be sure to have no blank lines between files Not This:
* [Chapter One](chapter-one/README.md)
* [Chapter Two](chapter-two/README.md)
* [Chapter Two Article One](chapter-two/article-one.md)Like This:
* [Chapter One](chapter-one/README.md)
* [Chapter Two](chapter-two/README.md)
* [Chapter Two Article One](chapter-two/article-one.md)