Well.. OCR is a challenging problem, at best.
Also, there's a, probably separate issue, often seen with PDFs (but more the ones that are composed as such, not OCR I think): some tools optimize the font / character set, only to what's used, or I suppose sorted by frequency of usage or whatever. You can read perfectly legible text on screen, but select and copy it and it's just gibberish -- albeit a simple substitution cipher, but pretty well useless for copy-pasting anyway.
I don't know which of these problems eBooks have; evidently given your experience, they rely on the OCR, and perhaps built-in fonts, to show documents. So a faulty OCR is truly fatal to the experience.
Tim