I found the kindle version of Stone and Anvil had about three chapters in the middle in the wrong order. Really confuses the story. I had to compare it to a print copy to figure out what should be where. I reported it to Amazon, who said they'd notify the publisher. That was about six months ago, and so far no update.
Well, it looks as if Stone & Anvil
has already been updated as part of the program I mentioned back last November. So, either the changes you mentioned have already been made or they were missed and are still there in a cleaned-up prettier version. The version you mentioned that had the chapters out-of-sequence, did it have the "Thank you for purchasing this Pocket Books ebook - Signup Here" page in the front and back of the book? If not, you were definitely reading and older version and a newer one is available. You may just try re-downloading to see if they send the newer version.
Turns out it was After the Fall, not Stone and Anvil, but yes, it does have the pocket ebooks "sign up here" pages.
I've tried re-downloading the kindle book, and the issue is still there.