How about the BIGGEST incontinuity where when your flying with Harry, its obviously daytime, yet in the forrest & womping willow scenes, its suddenly night time? That might not be whats intended, especially due to lighting issues, but from a spectators point of view, thats how I see it.
You've got to keep in mind that in the books, the forest was described as being so thick that it appeared to be night time in the middle of the day in some parts as I recall. It's supposed to be a pretty dark place. I totally agree with you on the Whomping Willow scene though, although that might be forgivable for the 'storm' that began during the Quidditch match.