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.
Alternate Character Interpretation: The aliens. Their complete lack of armor and weapons is usually cited simply as an example of What an Idiot, but some more serious hypotheses have been put forward. The two most prominent are that they aliens were actually peaceful, and only began attacking humans after the humans were aggressive towards them, and that they were actually demons defeated by holy water.
Or simply that we're not supposed to understand why. The movie is attempting to convey an alien invasion not from a gutsy action hero's perspective who blows stuff up and saves the day, but from a normal family who's just trying to hunker down and live through it. We don't understand why the aliens do what they do the way they do because said family almost certainly wouldn't have any clue.
In-Universe, the radio personality speculates near the end of the film that the aliens were only committing a massive raid and not trying to invade or conquer the planet, citing that he saw them drag a man and his family into their ship as evidence.
A less serious interpretation is that this was the aliens' version of a frathouse prank, akin to forcing a pledge to try to, say, get honey from a beehive naked or something.
Big Lipped Alligator Moment: The scene in which Graham and the kids come across an illustration in Morgan's book that shows a house that looks just like theirs set on fire, with three people (a man and two kids) lying dead outside it. The scene is pretty lengthy, is filled with ominous music and set-up, and yet it's never explained or brought up again.
Hell Is That Noise: That clicking, almost-but-not-quite normal sound coming from the baby monitor? It's the aliens.
Hilarious in Hindsight: The scene where Graham finds it hard to cuss and scare intruders off his farm was already funny in the first place. Post Mel Gibson's widely publicized, coarsely worded fits? Hysterical!
Idiot Plot: As mentioned... everywhere, the aliens invading a planet that's covered in 70% water without wearing so much as shoes when water is completely toxic to them, don't have weapons, and are easily captured, outwitted, or outsmarted by random people.
It Was His Sled: Even those who have not seen the movie are often aware of the twist. Shyamalan movies in general are vulnerable to this.
Memetic Mutation: The disturbing "It's Behind" scene is probably the most parodied in the movie, due to its over-the-top drama and suspense leading up to the alien's appearance. It was mostly parodied on YTMND, though.
Moral Event Horizon: The alien that stays behind does so because he wants revenge on Graham for cutting off his fingers. All right, that's understandable...wait, he's going to get revenge on Graham by attacking, with murderous intent, Graham's son? Dick move.
It is stated by Meryll that the aliens left their wounded behind so the alien at the end most likely didn't stay of its own accord.
Narm: The movie would actually be a pretty good thriller if it wasn't for the mind-numbingly stupid decision to have the aliens be weak to water. Also, Bo's bizarre behavior fluctuates pretty wildly between being genuinely unsettling and so over-the-top it's goofy.
Nightmare Retardant: One of the more infamous cases. The direction surrounding the aliens is genuinely creepy, but by the end of the movie, you realize that you were cowering in fear of a monster that's barely stronger than a normal human and would treat a garden hose like a flamethrower.