They are unable to index every occurrence of words in the text. They have problems correctly alphabetizing the entries. They cannot distinguish between trivial occurrences of a term and significant or pertinent occurrences of a term. They do not adequately define the entries that they include. Just the ones where the word is the main focus of discussion or where important information about that word is added.
Readers expect to be able to scan all occurrences of the word to find what they are looking for.
You only index occurrences of the word in the chapter or section where it is the main focus. This enables readers to find the main information on that term. Important detail about the term may occur elsewhere in the book other than where it is the main focus. Point readers from the synonym to the preferred term. Point readers to related terms.