Let's start with the obvious: The fact that Harry has to wear glasses is frickin' ludicrous. It takes place in a world where they can regrow bones! They should FOR SURE be able to figure a way to fix people's eyesight the second it started to blur. I mean, muggles have lasik! Every wizard in Hogwarts should be able to reproduce that same basic procedure with their wand.
I like a nice train ride as much as the next guy, but that shit is nowhere near as efficient as some of the other forms of transportation demonstrated in the wizarding world. Portkeys, for example, also take a person between two set locations, but unlike trains they do it in a goddamn instant. Sure, you replace a lovely trip through the English countryside with a jarring experience that leaves you feeling nauseous, but I'd barf for an hour straight if it meant getting where I wanted to go in seconds flat.
This is a small quibble, but that doesn't mean it doesn't fill me murderous rage: At least one point in the film series, Mrs. Weasley is depicted as using an enchanted spoon to mix something for her while she does something else. Here it is look:
If she's going to use magic there, why include the spoon at all? Why not just use magic to mix whatever's in that damn bowl? The fact that she uses godlike powers to propel a wooden spoon feels insanely illogical. It would be like if we used all our technology to create robotic mailmen instead of just inventing email....actually while we're on the subject...
Why do wizards still have a postal service? More specifically, why is the wizard's postal service entirely bird-based? It's like having a mailman who eats live mice and shits in your room. Also why would a wizard want to wait for an owl when they can just summon shit? Furthermore, if for some reason they decide that they don't want to use their godlike powers to communicate, there should still be at least 12,000 options for things to use before they settle on owls. Not only are they clearly slower than your average wizard on a broomstick, but they're also a bitch to raise. I don't care how badass Hedwig is, if we're being rational, he's clearly not worth the effort.
When you stop and think about it, the character Filch is incredibly messed up. Because he's a squib he's resigned to be the caretaker at Hogwarts which seems fine until you remember that he's probably the least suited to the job out of anyone at that school. Imagine how easy cleaning would be with magic? Now imagine instead of just waving a wand and making everyone spick and span, you instead had someone spend their day doing it, all by hand, surrounded by a bunch of snotty little kids in capes. It's pretty fucked up.
There are a lot of writing implements out there, and the quill is BY FAR the worst of the bunch. WHY ARE WIZARDS WASTING THEIR TIME WITH THEM!?!?!?! Let's say for arguments sake, that there's no spell they could use in order to put words on the paper, even though that's obviously not the case. Couldn't they have at least come up with a way to write that doesn't require carrying around a bottle of ink? I mean, they figured out time travel!
Speaking of time travel, why did the wizards turn a blind eye to the holocaust? World War II is canon in Harry Potter, which means that every goddamn wizard in the world has blood on their hands. I understand not wanting to interact too much with the muggle world, but the second that mass genocide comes into play, they should suspend this rule just a little bit. All they'd need was a time turner and a wand and they could prevent some horrible shit from happening by simply yelling "Avada kedavra" at baby Hitler. Honestly the fact that not one wizard did this suggests a stunning disregard for non-magical life.
One of Ron Weasley's defining characteristics is the fact that his family is kind of poor, and that makes absolutely no sense. Economic inequality should not be a thing in this universe!!!!!!!!!! Why is Ron forced to walk around in beat up hand me downs when he lives in a world where most people can make anything they want by pointing a piece of wood at it? If Professor McGonagall can turn herself into a cat, surely Ron's parents can turn his sweater into a less shitty sweater. For Christ's sake, Hermione fixed Harry's broken glasses when she was a damn first year! Maybe the Weasley's will never be as rich as the Malfoys, but their quality of life should be significantly better than it appears to be in the book.
J.K. Rowling famously stated that wizards practice all sorts of real world religions, and it's like how. What the fuck wizard is practicing Christianity? I was raised Catholic and I can tell you that a lot of it was rooted in the idea that Jesus performed miracles that were nowhere near as impressive as what your average first year at Hogwarts could do. Imagine going up to a goddamn wizard and telling them that they should worship someone because they turned water into wine? They'd laugh in your face. I can understand wizards creating their own religions but the fact that they're practicing our boring real world religions makes no sense.