That's exactly the case. Novels take a long time to get done, so the first several novels in each of the TNG through ENT novel lines were written before the shows had premiered or even completed filming, and thus the novelists had to make do with what early material was available -- which in the case of Ghost Ship was just the bible and the pilot script, IIRC. And TNG changed a lot from the initial bible due to all the chaos and turnover on the writing staff.
Part of me wants to bring up the Broken Bow novelization again...
One occasionally hears rumors of an author getting to see an early cut of a movie or episode, but I've never actually known that to happen in all my years of writing and editing novelizations.
The only exceptions I can think of are the Ramsey Campbell novelizations of some of the Universal Horror films, the second novelization of The Terminator that was done right before T2 came out, and the most recent Star Wars novelizations that are coming out months after the films. All of these are unique situations I don't expect to see duplicated elsewhere, especially since adult novelizations are such an endangered species these days.