Most of those issues I mention are exactly the kinds of issues which pull the reader out of the text, even though he may not be able to pinpoint exactly why. Certainly often when I use Instapaper to read a web page or Calibre to convert ebooks I can read through the issues if I try hard enough, but it takes more effort than reading a well-produced book, and I somewhat regularly give up on automatically-converted texts because the issues are just too dire.
(Some of my other favorite conversion errors: Endnotes or references not hyperlinked. Chapters and other headings not correctly marked-up. Page numbers or other irrelevant header/footer material not stripped. Footnotes, margin notes, or other relevant header/footer material stripped. ...As you can tell, I'm great fun at cocktail parties.)
