One infamous one in Doctor Who is Campaign. It was a book that was commissioned by BBC Books on the basis of a synopsis however Jim Mortimore veered wildly off the synopsis which resulted in the book being cancelled. The download that I've linked even includes a section at the end that explains how the book was written and why it wasn't accepted. Just bear in mind that it was written by Mortimore so we can't say that his view of events is what happened.

It's a very weird book, the basic concept was the First Doctor, Ian, Barbara and Susan meet Alexander the Great but are scattered throughout time and have to find each other. Given the reason for cancellation, the book as written is not that.