That post about Star Trek novels brought to mind one of my pet peeves, and it's something the books are guilty of. A massive "series", if you can call it that, where there is no real continuity. One author will contradict another, and so forth.
Another series that is really bad about that is the Dragonlance series. You have the original trilogy, the follow-up trilogy, and books that came after that all written by the same team of two. You've got spin-offs written by many different authors, going in all different directions, but apparently those aren't "true" canon. Adventures concerning the main characters are accepted as part of the series, but apparently aren't to be taken seriously. Some of them were my favorite books in the series. Not too many new books are coming out for that series these days, but it contradicts itself a lot. That said...I still like it, and I'll occasionally pick up one of my old books to read for nostalgia. Also, reading the books as an adult, I strongly believe Raistlin and Kitiara to be sociopaths, and the scary thing is that they're two of the most popular characters!
Another thing that bothers me has to do with poor editing. The wrong character name being used, among other things. For example, the person speaking addresses someone by their own name. What, are you talking to yourself?
The only time I've ever defaced one of my own books, it was to correct errors like that with a pen.