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.
Designated Villain: Secretary of Defense Regina Jackson, one of only a couple of characters who display any common sense and intelligence at all in the film.
She attempts to interrogate and vaguely threatens a representative of a race powerful enough to wipe out humanity just by forgetting to hit the breaks when it enters atmosphere.
Debatable, all she wants is a battle, no matter how irrational it is.
Esoteric Happy Ending: Klaatu agrees to spare the Earth and humanity, but only after he generates an EMP so powerful that it stops all technology on Earth. Given how technologically-dependent our whole society has become, it's more than likely that mankind will plunge into a dark age with millions, perhaps even billions of deaths. But at least Jacob finally called Helen "Mom", right?
Fridge Logic: So, the aliens have had a spy with us since 1920, long enough to bond with us, but he doesn't bother telling alien!Keanu of our capacity to mourn our dead and to love our (step) children even though that's precisely the data that ultimately causes us to be spared.
Aliens come into planet, first choice, though they don't have any visible weapons of any kind is shoot shoot shoot!
Nightmare Fuel: A scientist is trapped next to the Gort as metal locusts are eating him away.
Tearjerker: Jacob's futile request for Klaatu to bring back his father, and Jacob and Helen's reconciliation afterward. It's so tearjerkery it makes Klaatu decide not to destroy humanity.
Apparently, the thing that makes humanity worth sparing is our capacity for emotional schmaltz.
Strawman Has a Point: Various characters from the government and military are depicted as being callous, paranoid, and inhumane when they immediately imprison the injured alien visitor and attempt to interrogate him about what he's doing on Earth. Even though the viewers are supposed to be disgusted with their behavior, there's one minor problem; Klaatu is indeed planning to destroy the entire human race, taking all of a day and a couple interviews to verify it as the right course. The "inhumane" government officials were completely correct to treat him as an enemy.
The opposite is also true, the humans act out and wind up the aliens even though they had no clear weapons and were not clearly attacking them.