Some of the ebooks I've bought or sampled through the Kindle store had formatting problems I have never seen in print books! It's more of a problem with older books than new ones. Only a couple of times have I had any problems with a recent book. But I'm convinced that when a publisher releases an older book on the Kindle they're not even looking at it!
My annoyance level varies with the price I pay, of course. I don't expect a lot when I convert a free PDF. When I bought an old, way out of print Andre Norton book for $2.00 or so, the formatting glitches were annoying enough that I deleted that copy of book and paid a little more (about $4) for a better copy from a different publisher. But when a publisher (Sourcebooks, I'm talking about YOU!) releases a Kindle version of a Georgette Heyer novel and wants almost $10 for it, I expect good, clean copy! This is not a book that's out of print, so I'm not desperate to get it. I am not paying that kind of money for a book that's a) not a new hardcover, b) by an author who has been dead for decades and c) seriously flawed in that the paragraphs don't indent. Book style calls for paragraphs to indent for a reason— it's hard to read without that! If they had looked at it, they would know that.
I don't know whether it's Amazon's fault or the publishers, but somebody needs to get cracking on this. Maybe Amazon should give every publisher a free Kindle so they can look at their own books? If it weren't for the "Try a free sample" feature, I would be truly steamed, but as it is, I have learned to always look before I buy.