To answer your main question the point is that someone has spotted something in the plot/story line/character element that didn't make much sense to them and so they want to know the answer. It really is as simple as that.
However, to go a bit deeper and expand on your reasoning.
My POV is that many works of fiction (especially from popculture) disregard reality and common sense.
There's a couple of points to this so:
Exactly this is your point of view and as I'm sure you know not everyone has the same point of view.
Maybe they do disregard popculture but a lot of readers/watchers watch these things because of that. Not everyone just wants to immerse themselves in something exactly like real life... a lot of people immerse themselves in another work to escape reality.
This is either because they think that this attitude will make their works more interesting or because the writers themselves (with all respect to them) have no clue what they're talking about and are thus unable to come with a believable plot.
To be honest a lot of the time the slightly less believable part of the plot opens up more pathways to a more interesting story. I'm certainly happy to suspend my disbelief over some minor "problem" if it leads to more interesting outcomes in the end. Also not everyone knows everything, writers generally have a good grasp of "most" elements of the story but they won't be an expert in everything they talk about so things won't always be "correct". For example, it's well known that JKR is bad at maths.
I think it's also worth pointing out that these are fictional worlds, it's not a surprise that not everything works the same. The next point is an important one and something that comes up a lot.
People are a lot more likely to question something that is closer to reality.
Dragons exist in this universe? Wow cool I can believe that! That dragon took a trip that should have taken 5 days in 3 days!? WHAT THE HELL IS THIS NONSENSE!!11!!!!???
In both cases the result is that trying to find any sense in a plot that makes no sense is, well, senseless. Asking such questions is precisely as pointless as asking how could Jessie, James & Meowth not die each time they were launched into orbit and fell back on Earth.
Is it? If you "know" it "makes no sense" you likely wouldn't be asking because you'd "know" the answer. The people asking these questions are asking because they don't know the answer. Even if they do know the reasoning behind why it makes no sense maybe they are hoping they skipped over something wherein fact it does make sense after all.
So that's it from a questioner's perspective but why do people answer these? There are any number of reasons but to list a few in line with your question:
They say it doesn't make sense and why it doesn't make sense.
They attempt to explain how it could make sense.
They tell us actually it does make sense after all because of X, Y and Z. In fact a lot of very good answers can come from a question that started off as a false premise.
It's worth noting that the second of these questions is currently in the HNQ and considering the score of the first it likely was at some point too. So, whilst SFF users liked the questions initially their scores have exploded exponentially due to the effect of the HNQ and the drive by users it brings in.
How can every Cubone be wearing its dead mothers' skull? This is actually quite a nice question when you think about it. How can this actually be the case? And before I look at the answers (and knowing nothing of Pokemon) I can think of a few in universe possibilities:
- They can only have one child
- They wear only part of the skull
- Can grow multiple skulls
- They die after giving birth
The actual top answer goes into a lot of information and is very detailed. If we had not had this question asked we would have lost out on this. It even comes to a sensible in universe reasoning, the Pokedex is inaccurate and potentially incorporates myths as fact.
Why did Dumbledore allow Draco Malfoy to return to school in Harry Potter and the Half Blood Prince? Again it's quite a nice question that will lead into answers that analyse Dumbledore's character. The question itself isn't actually inherently bad if asked about today's schools, in the UK students are given a lot of chances to improve their behaviour before expulsion and of course before accusing someone of attempted murder you need to have evidence.
Then looking at the answer it is very nice and detailed with a good assessment of Dumbledore's character and why he let this happen. It in fact shows us that there perhaps the plot _doesn't "disregard reality and common sense".