These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Idiot Ball: The groups initial plan to head to the yacht, since the aliens aren't over the water. Because a single boat on the water wouldn't be an obvious target to a race that have machines that can fly!
One-Scene Wonder: The Stealth Bomber is generally agreed upon to be the coolest scene in the movie.
Some people have even commented that the Stealth Bomber was the best character in the movie!
Special Effects Failure: If you look closely the first time Turk, er, Terry shoots at the lock, literally nothing happens to the door.
Squick: The aliens in everything they do, but especially the giant, four-legged collectors. They harvest people by grabbing them with a tentacle that shoots out from their feet. Once caught in the foot, the victim is forced inside by all four equidistant toes shoving them in with a sickening crunch.
The Untwist: So a hyper advanced race of aliens invade Earth, decimate our defences, rip our military forces apart and begin abducting humanity because their batteries are running out of juice. How will our race defend our right to survive and prevail against this evil force? We don't.
They Wasted a Perfectly Good Plot: One of the brain-powered death machines regaining its humanity and fighting to overthrow the monsters who threaten to do this to everyone on Earth? What a great story! ... Wait, that was just the last five minutes? Crap.
Editing out the characters and focusing entirely on the military, media coverage, and other humans getting caught makes for a fairly interesting visual story of mankind's struggle to survive and fight back.
Villain Sue: The aliens to an unbelievable degree. Absolutely nothing stops them, they brush every attack, and the heroes completely fail to fight back against them. Probably the biggest moment is when the aliens manage to shrug off a nuke without any trouble.