OH PLEASE
they alien ships were buried???!! come on we never noticed them - sorry not in the novel they landed in ships like the first movie.
ALiens BEAMED into these ships - sorry they physically landed again in ships
Tom Cruise has to tell the military that the shields were down - sorry her majesty's military figured that one out in the novel as well.
Aliens looked like ID4 aliens - sorry they were more squidlike and had beaks in the novel.
they kept certain SCENES from the book that did not work - the ferry was in the book since people were trying to flea the British coast - who the heck decides to head for a ferry that moves slow when you can head to the interior with more places to run
The first movie adapted the book in a much more realistic way.
Niggling plot holes aren't all that important in a film like this which sets out to do nothing more then induce tension and suspense. It's filled with one visual inspiration after another. No one knows where to put a camera like SS.