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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.
Or: Sufficiently Advanced Aliens with Blue and Orange Morality and the sideways logic to compliment it tend to work In Mysterious Ways. This could be why stuff didn't make sense to most people raving about Plot Hole issues. It doesn't make sense to us because we don't think like they do. They were trying to help (or save what they could of their experiment, if you want a sprinkle of Nightmare Fuel with this) before everything was destroyed, but because of some seemingly arbitrary (again, to our logic) rule, they couldn't interfere with the development of humanity until literally the final hour. The possibilities for why are endless and impossible to confirm.
Alternatively, if one assumes the Strangers are as much bound by You Can't Fight Fate as much as the humans but are able to perceive preordained events (hence the list), then every illogical thing they do actually makes sense, since they are being forced to do these things because they've already seen themselves do them.
Angst? What Angst?: Abby seems to take the death of her mother remarkably well, when she was only killed while trying to save her daughter from a situation that was caused by the Strangers. This is also completely at odds with their claim that the Strangers "don't want to hurt us".
Unless she was being very specific about the "us" part.
The disasters we witness. For example, the plane crash. Most films go for the flashy initial crash; this film actually bothered to show the immediate aftermath of such an event: Passengers screaming from inside the wreckage, people running, people on fire, people just walking in shock, people trying to crawl through fire to escape what's left of the cabin, burning bodies scattered about...one shot had a bunch of people running from one of the few intact parts of the plane; you think they're safe, then BOOM!! they're enveloped in flames. And in the middle of this horror show, our protagonist, trying desperately to do what little he can to help, until rescue workers finally pull him away.
John: "I keep seeing their faces...burning..."
This is capped by the final disaster - the killer flare, though it's not as high-octane as the earlier, personal disasters, the lead-up is incredibly creepy: The glowing night sky and lighting storms, the brown aurora borealis in broad daylight the following day, the sun getting brighter and brighter, the riots and panic, useless EBS alerts over the TV and radio. When the final firestorm comes, it's incredibly fast; nobody, including the protagonist, suffers long once it hits. Perhaps the worst part isn't the depiction of the actual firestorm, but the atmosphere being blown away. If anything survives the scouring by fire, there won't be any atmosphere left to support life. No, the caves wouldn't have saved them.
The vision Caleb sees the entire planet on fire, herds of animals fleeing in panic as they burn alive. Holy freaking hell.
Paranoia Fuel: The people shaped things watching the kids. Never mind they're supposed to symbolize angels. They are creepy!
Shocking Swerve: When the strange, scary people showing up to the children and others turn out in the very end to be benevolent aliens (or angels) who are going to take them away and bring them back later to reseed the planet post-Armageddon.
Although the benevolent part is debatable given how at odds it is with their behaviour.