Unfortunately, this problem is not unique to Kindle. It occurs with the Apple bookstore as well, and even here on Eat Your Books. ISBN cataloging numbers change with edition and the systems aren't smart enough to catch inconsequentlal changes. Sometimes there is a good reason for the different editions (new editions) and sometimes not (hardback vs. paperback, like you can tell the difference in an ebook).
I recently was surprised that I was the only Eat Your Books member with a particular Graham Kerr cookbook. He was very big in his day. And it was a hardback cookbook published by Doubleday! I dug a little deeper... and there is an entry for a spiral bound version of that cookbook, and a number of members have that editon.
Jamie Oliver's "Comfort Food" has different subtitles in the UK and US editions and far more folks own that UK edition (home field advantage for Jamie I assume).
And more generally with both Kindle and Apple iBooks, I have found that books I know I purchased, later fail to show up in my library. I'm guessing that an edition is replaced by a subsequent edition and the older is no longer in the catalog. I have managed to get this straightened out when it was important, but still very annoying (and time consuming). Hopefully this is all 'growing pains' and the publishing industry will get it's act in gear.