If you check out the change list from my edit of Chamber of Secrets you'll find the official extended cut introduces a lot of flaws that should have been fixed.

Also, the Malfoy crap in HBP: if you check out the original script you can see they recycled some footage (Malfoy pulls an extremely dusty cloth off of the vanishing cabinet more than once) and split up the Malfoy scene to try and extend it suspense or something.

In most cases I've found the scripts to be better than the final cuts and they reveal many of the flaws. They make great guides to help you edit around those flaws.