"Why are there so many mistakes in the e-versions of print books?
[...] 'In the print book production process, typesetters work from an author's word processing files that have been electronically edited and are ready to proceed to the next stage: formatting and page layout. [says Maggie Dana]
Typesetters strip the author's codes and import these word processing files into page layout programs, such as Adobe InDesign or Quark, and massage them into attractive book pages per the publisher's design specifications. At this point, all connection with the author's original files is lost. Any changes made from this point forward are made solely inside the page layout software, NOT in the Word document as well. It is not a parallel process.
From these page layout documents, typesetters generate PDFs to send to the publisher as page proofs. The publisher and author mark their corrections on the PDFs and send them back to the typesetter, who makes the changes. There are often several rounds of proof corrections going back and forth before everyone is happy. Therefore the final PDF that goes off to the printer is often quite different from the author's original Word files.' "
— Karen Dionne, Huffington Post