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It depends on the book.
Like you noticed, the better books are made directly from digital files. Someone who knows what they're doing will assemble a set of HTML files with properly proofread text and formatting and layout (table of contents, footnotes, images and such) and carefully turn it into an ePub or convert it to a Mobi. A few typos may slip through, but overall the job is well done.
Other books, some lazy person just takes an OCR file from a scanned book and slaps it up into an ePub or Mobi, not really bothering to actually read and check for typos or punctuation in the wrong place. Sometimes for bonus amusement, they'll run a search-and-replace for certain words, which can yield unexpected results if the words they replace aren't actually misspelt and they've replaced them with completely different words. Then they wait for reader complaints to roll in, which is apparently when they bother to start fixing things, if at all.
The third approach is taking a Word document and running it through Smashwords' very aptly named "Meatgrinder" to auto-generate the resulting e-book files which are sometimes passed on to Amazon, B&N, Sony, & Kobo via the Smashwords Premium distribution system. Errors are generally not the author/publisher's fault; they did the best they could with what they were given.
Hope this helps.
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