I have found a number of ebooks that I have purchased have some glitches in the encoding. Most often I notice that the pages are mapped incorrectly. For instance, in one case I advance to the next page from 121 and it returns me to 117. In another instance, I advance from 91 and it takes me to page 192. The pages all exist and going in the opposite direction does not seem to have the problem, though I have found a few cases where it did have quirks going backwards as well.
Is there a way to correct this locally without stripping the DRM, finding the incorrect encoding, and fixing it manually? Is there an established channel to go through for reporting these glitches?
There is not a way you can correct an ebook without removing the DRM and adjusting the code. Depending on where you purchased your ebook you should contact their customer service and they will require that the publisher/author correct the issue and issue you a refund.
As an ebook developer for a large publisher, I recommend contacting the publisher. The best method is probably the customer service contact on the website. When I hear directly from a customer, I try to correct the issue that day.
I build a lot of flowing ePubs and I have had a lot of this kind of error happening when proofreading an open ePub folder, for example with Book Proofer for Mac. The errors most often show up at the end of a chapter, causing me to turn the page several times with old pages showing up before moving on to the next chapter.
Weirdly enough, the epubcheck and code check has returned no errors, and when actually checking the finished book there are no such problems. So I'm thinking it could be device or app specific.