1. I've seen in Harry Potter fan fics the theory put that Harry did not do well in primary school because his Aunt and Uncle would get mad at him. Harry then continued to do so and be lazy at Hogwarts because of his friendship with Ron and trying to fit in. I rather like that theory but it seems that he really is that lazy, which he should have stopped being so when he learned that Voldemort is trying to kill him and so that he would make his parents proud (after all it is said that his mother did very well in school). In the first book, Harry considered his school books very interesting, and read them late into the night during the month before he went off to Hogwarts later he seems to be a serious slacker.
2. Why is Hogwarts: A History the only history book ever mentioned in fan fics? I also don't get why Hermione would want 10 copies of the book. We are told there are other magic history books (Hermione mentions reading about Harry in several of them in her very first appearance) and Harry Potter has actually read at least one of them in the books: He found the name Hedwig in History of Magic.
3. Why didn't Hermione ever call Harry over the phone or contact him via the post office? Harry gave Ron and Hermione his phone number at the end of book 2 and Ron who doesn't know very much about muggle technology calls him. Why didn't Hermione do so? It would make a lot more sense after all being muggle born the idea of using the post office or phone should be second nature to her - the use of floo powder or owl should be what she has to think about to use since she only recently had learned about their existence. Muggle means should have been familiar to the point of knowing them for longer than she could actually remember.
4. The magical money system shown in the book makes no sense based on the shown purchases. The Weasley's, namely Ron, could not afford a good wand. The single most important item that a wizard/witch will ever have or need. Wands being very expensive makes sense though in Book 1, Harry pays 7 Galleons for his wand. In Book 2, Mrs. Weasley takes 1 Galleon and a pile of Sickles from her vault to buy all of her children's school supplies. In book 3, Hermione notes that she has 10 Galleons left over after her school shopping to buy a birthday present. So she must be pretty damn well off since she has nearly 10 times as much money as left over than the Weasley's had total for school supplies and an unwanted (the store didn't seem to want the cat) magical breed of cat costs more than a wand (again the single most important item a wizard will ever need).
5. How does anyone know what happened when Harry's parents were killed? Heck how does anyone even know that Harry survived the killing curse since Harry was the only survivor (it is mentioned repeatedly that he was the only survivor) and wasn't able to talk about it. Who told people that Harry went to live with his muggle relatives and his having a scar on his forehead?
6. I've seen fan fics mention that a simple shield charm would easily stop bullets. This may or may not be true since we don't see anyone try to block a bullet with one though other than Voldemort's at the department of ministries we don't see them block any physical objects at all only energy. The thing I find annoying is the claim that any wizard/witch will easily produce a shield and automatically win versus a bullet. While I do not know the exact quote J K Rowling has mentioned that a person with a gun will beat a wizard (bullets faster than spells but the person has to be carrying the gun, prepared to use it in the situation, etc.). Though really the reason I dislike the theory wizard beats muggle with gun because of shield is because it is stated in the books that most witches and wizards can't produce a decent shield charm which is why the Weasley twins shield hats sold so well.
7. I actually liked that Voldemort split up his soul and placed it in several objects (called a Horcrux). What I didn't like at all is that Harry had one in him. Splitting your soul and placing it in an object should not be able to be done on accident and I would imagine it to be extremely hard to do (multiple steps would pretty much have to be needed and killing itself could not possibly automatically split a persons soul since if that were true Voldemort and all the death eaters would have done so dozens of times). I also didn't find Voldemort's protections on them to be very good (could have sent one or more of them to some place extremely far away from England for example) and his plans to use them to be restored to life in case he died didn't seem to really exist (if he had plans to restore himself you'd think it wouldn't have taken him so long).
8. I've seen a few fics in which a court setting is used. The thing is the court setting is usually very different from what is shown in the books. Judging by Dumbledore's memories of Death Eater trials standard practice in the wizarding world is to arrest people and lock them away with no contact from anyone until their trial. Defense lawyers/counsel doesn't seem to exist in that world either since the accused followers of Voldemort had been chained to chairs at their trials with no defense counsel or representation of any sort. Also there is clearly no right to remain silent. There is corruption or a system set in place where you can buy your way out though.
9. Why would the majority of people seem to believe that Harry was making stuff up to get attention when he was already the most famous teen in the Wizarding World and had just won the Tri-Wizard Tournament? Also with him being so damn famous that books had been written about him and stories made up about him were bedtime stories where did all the gifts, letters, death threats, and miscellaneous other stuff people would have sent him over the years go? Celebrities much less famous than he is portrayed to be get a lot of mail. If it is being blocked and processed somehow why does some manage to get through for instance the broomstick from his god father (considering everyone thought he was a killer that should have been blocked)?
10. Why hadn't Harry or Hermione or someone contemplated leaving Britain? Considering all the crap that happened and the life and death situations that occur I would have done so.
11. Dumbledore instructed Sirius to gather up the old crowd. How would Sirius do that considering the fact that most of the wizarding world including the old crowd think he's a murderer and follower of Voldemort? Even if they didn't think he was a murderer by that point (which absolutely nothing shows) how was he supposed to get in touch with them since he couldn't move around freely since the majority of people still did think him a murderer?
12. Why didn't Hermione find the Bubble-Head charm prior to the second task? That really makes no sense to me since two of the other champions used it and in later books, like book 5 when dungbombs are released, many students use it. Hell why hadn't she found other means beyond the Gilliweed which she hadn't found? Were all the books that could possibly have been useful purposely kept away from her?
13. In the books Harry and Fluer waded into the lake still wearing robes most fan fics ignore this and have them wear swim clothes like the movies which makes a lot more sense. Why would Harry not have swim trunks or something at least better than robes?
14. While I don't like that Harry had a soul fragment of Voldemort's within him did Dumbledore even contemplate that there might possibly be a way to remove a soul fragment from someone other than having the person be killed?
15. Considering Harry's upbringing in which he was called names, picked on, and had nasty taunts directed at him why would he (or Hermione for that matter who as the first book shows had problems with those types of things even at Hogwarts) find Ginny's sense of humor attractive since it largely involved making fun of others, sarcastic putdowns, and mean-spirited pranks. Harry in my opinion really should have gotten mad at her for calling Fluer Phlegm and making fun of Fluer behind her back considering how much he hated to be called names like freak and how people treated him.
16. Why was Bill's and Fleur's wedding at the Burrow? First it makes a tempting target for Voldemort but really I think it should have been in France. Traditionally weddings are held in the bride's hometown and there is a traditional French custom for the groom to call on his future bride at her home on the morning of their wedding and escort her to the wedding chapel in a procession. Even beyond that weddings are more important to the brides than the husbands and with the way the Weasley's (namely Ginny and Molly) treated her she'd want it to be held where it makes her more comfortable.
17. When Voldemort possessed Harry at the department of ministries why didn't he just kill Harry by jumping out the window or something?
18. It really bothers me how Hermione believes books (and in authority) so much even after being proven that some books are filled with lies (Lockhart's). She is also not as open minded as I would like and hadn't found some stuff in books that I believe would have been easy to find. There is a reason I like (and find it at times the only damn possible way for somethings to make sense) the theory that muggle born are placed under compulsion charms.
19. Hermione is the one that states that electricity doesn't work at Hogwarts. I'm kind of wondering if that were really a truth (after all the castle had never been retrofitted with electrical conduits, with magic their isn't much need to do so, and the ministry/pure-bloods would be against it's use even if it could) or a lie told in a book she read and believed (or was compelled to believe which is entirely possible seeing how muggle born are never shown to even try muggle means like acquiring a fountain pen which would be easier to use than a Quill and the type of magic which could do so is shown to exist - hell just give all muggle born a book with a charm like those mentioned to be in the Black library).
20. Why does Hermione completely discount the possibility that the creatures Luna talks about exist? If they are made up or not real doesn't matter, her not even thinking that they are possible bothers me. They maybe invisible unless certain criteria are met like Thestrals that only people who have seen and understand death can see which she didn't think were pulling the carts. They maybe different names for existing creatures since many creatures have many names or be from a different part of the world in which she hadn't read about. Similarly why didn't she believe that there were voices coming from the death veil? She may not have been able to hear them but she also didn't hear the Basilisk in the halls (only Harry did, which makes it even harder to stomach Ron being able to fake snake language since some of it most likely isn't within the normal hearing spectrum) which was proven to be in existence.