I think that what does bug me (which is probably what you are saying and I was just misunderstanding because of my unconscious need to be disagreeable) is a bunch of hand waving, vague explanations that are supposed to be scientific and are meant to add credibility to the story when it appears that the writer didn't bother to learn anything about the subject. If they had even looked up the subject on wikipedia they'd have realized how inane their "scientific explanation" was.
Yes, exactly, you phrased it better and more clearly than I did, thank you. I recently was given a box full of books that I normally wouldn't read. In addition to the book that caused the above rant I found another one with an Atlantis twist that was extremely disappointing. The author found out one interesting fact about the mantle of the Earth and then put a lot of really old, tired cliches about people living in Atlantis (they are all incredibly beautiful, young, scientifically advanced, etc.). I know they turned out to be evil in some way because it was a thriller but I couldn't get far enough to find out what it was. They probably use regular humans to somehow fuel their advanced society, since that is the cliche that fits in with everything else.
I think I got spoiled by reading good science fiction and fantasy that the author has put a lot of work into so it is internally consistent and makes the reader think, e.g. Brandon Sanderson. Then I read bestsellers/thrillers that are just retreads of stuff already done and I get irritated. I guess I'm just cranky.