Check the comments after the post. That's mentioned as a possible reason and the author says that's not the case. Apparently Amazon is complaining about real hyphenated words, not line-break hyphen-ated words.
[edit: It appears, though, that the author is stylistically abusing hyphens, so while they may not be wrong, they're grating to most readers. So, should Amazon be in the business of banning books on the grounds of poor style, rather than technical grounds that are inarguable? (If the book contained the word hyphen-ated, that would be wrong unless it was dialogue and the speaker was pausing between syllables.)]
If "stylistically abusing" punctuation is worth of blocking an ebook, then I have to assume Huck Finn and Cloud Atlas are next on the list of books to remove for their heavily punctuated attempts to represent speech patterns.
furyg3 knows that the book only has proper hyphens. Amazon took down the book because they thought it was full of line break hyphens. It wasn't, but that's what Amazon thought because they never actually looked.
So really the title of the post should be "Collateral damage when Amazon went to war against bad punctuation," which casts Amazon's motives in a different light.
I don't believe that is satisfactorily disproving this position. It is very very easy to believe that the automated system trying to prevent lazy formatting is just interpreting a large prevalence of hyphenated words as line break hyphens.
Graeme merely asserts that his book was free of those, which we knew going in. It does nothing to say why Amazon was raising the issue, and it wouldn't shock me that an automated system would be unable to tell the difference.
[edit: It appears, though, that the author is stylistically abusing hyphens, so while they may not be wrong, they're grating to most readers. So, should Amazon be in the business of banning books on the grounds of poor style, rather than technical grounds that are inarguable? (If the book contained the word hyphen-ated, that would be wrong unless it was dialogue and the speaker was pausing between syllables.)]