Whenever you see bad formatting, it's almost always the publisher's fault. Amazon just serves the files that the publisher sends them.
The only time they get involved in the conversion is when the dreaded Topaz format is involved, and that's because the publisher pays them to do a cheapie scan job to hack up an image-based format which apparently costs less than making a "real" e-book. Also, both of Amazon's native formats and the tools they supply for conversion are kind of lacking, but that's only an excuse for occasional layout issues.
Chances are, if it's typo-riddled on Amazon, it's probably just as bad in ePub, too. B&N will at least let you download a sample if you're morbidly curious.
But considering the zillions of Star Trek books out there, I don't think all of them will be that bad. Diane Duane's Doctor's Orders (only $2.79 for Canadians!), which I got a Kindle sample of awhile ago, has a TOC, chapters starting on new pages, no really obvious typos in the text, and otherwise seems perfectly fine.
Maybe yours is just from a batch back when Simon & Schuster were being lazy with the e-book production and/or outsourced to a company with no standards. Or maybe they're secretly all riddled with typos lurking for the unwary buyer to spring after the sample text ends. Who knows?
If it's really bothersome, just contact Amazon Customer Service to tell them about it, and chances are they'll a) offer to send your complaint on to the publisher, b) maybe even offer to refund the book.
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