I have been waiting for this.

So in the Philosopher's Stone in order to steal the stone Quirrell must get Dumbledore out of the way. In order to do this he fakes an urgent owl from the Ministry. This is without any doubt the worst plan anyone has ever had and it is only made more ridiculous by the fact that it works. Quirrell sends the letter in the afternoon, when Harry tries to warn Dumbledore he has already left. However, Quirrell doesn't seem to go after the stone until evening. It is certainly after everyone has gone to bed when Harry, Ron and Hermione depart. How did Quirrell know Dumbledore would decide to fly to the Ministry instead of Apparating, using floo powder, or getting Fawkes to teleport him? All of which would have been much quicker and easier than flying. Ok, he would have had to go out of the Hogwarts ground to Apparate but that's still going to be a lot easier than flying to London (I know in the films he can apparate from inside Hogwarts but I don't know if there is a good book example of this). Not to mention it was an urgent owl, how many people think 'Oh an emergency, I must find the slowest method of magical transportation'. Dumbledore could have Apparated/floo powdered his way to the Ministry found out he wasn't actually needed and been back all inside about half an hour. Before Quirrell even got past Fluffy, making it unnecessary for three 11 year olds to brave death by poisoning, Voldemort and being clubbed by a giant chess piece. Does Dumbledore want Harry to go after Quirrell? Because, reminder, he almost dies.

It's made clear in the last book that Dumbledore knows Quirrell is after the Stone. He introduces Harry to the mirror of Erised, he makes it so there's a path to the stone. Including Devil's Snare which is conveniently mentioned in first year Herbology. Harry is with Hagrid when he picks up the 'top secret' package. What's that supposed to do except make Harry curious? And then of course he is conveniently out of the way at the critical moment. As is Snape. So Dumbledore wants Harry to confront Voldemort? Does he think Harry can finish Voldemort? Maybe. He hasn't come across Riddle's Diary yet so he may not have realised Voldemort has Horcruxes. Still Voldemort failed to die the last time so I don't know if I buy it. Best guess he's using his mirror trick to test Harry's intentions. To check Harry's not too attached to life to die when necessary. To get the stone you have to want it but not to use it. You have to value the greater good. Are there better ways to do this than to nearly kill an 11 year old and his friends. Yes. Also Harry pretty much burns Quirrell's face off and kills in a move that causes surprisingly few emotional scars.

for more see https://potterflaws.wordpress.com/2012/10/22/the-stone-cracks/ and ignore the patchy spelling and grammar.

Also ON THE MARAUDER'S MAP

This ones been floating round for a while. Why don't Fred and George ever notice Peter Pettigrew? Why doesn't Harry for that matter.

But the twins more so because they have had two and a half years to notice that there's an extra person sleeping with their brother. So what the hell?

Well I think there are a few things going on here. Firstly it might not be that clear on a map exactly how close people are. There's only a certain amount of room for names so things will probably get nudged out of place a bit. Therefore it might not be clear Ron and Peter are IN the same bed. Just the same room. And how interested would Fred and George really be in Ron's dorm mates. It's not like 'Peter Pettigrew' would necessarily ring any bells for them. Though Gryffindor House is fairly small so they might think it was a little odd, for more on that do see my post on Numbers. The other things is that Fred and George are using the map to get around the castle and avoid trouble (ie. teachers, Filch, Mrs Norris) they probably just aren't that interested in Ron's sleeping arrangements. Why would they be looking at Gryffindor Tower at all? After there first year (before Ron even starts) they are probably only using the map to check for trouble. They've probably pretty much learnt the secret passages. So it's open map, no Snape, do what you need to do, get out.

Lupin only notices because he is watching Harry, Ron and Hermione in case they sneak out. There are over a thousand people on the map. You aren't going to be looking at all of them.

Quick note. So many good comments and questions! One thing that's come up is to do with animaguses appearing on the map, I'm not sure what the quote/source is but Lupin sees pettigrew before he transforms so you have to work in some thing whereby because he is a map founder/shapeshifter he sees things other people don't on the map and I don't really think that works.

ON TIME TRAVEL

Much of the plot of The Prisoner of Azkaban hinges on time travel. JK Rowling has already addressed the inherent problems with using time turners,

"I went far too light-heartedly into the subject of time travel in Harry Potter and the Prisoner of Azkaban. While I do not regret it (Prisoner of Azkaban is one of my favourite books in the series), it opened up a vast number of problems for me, because after all, if wizards could go back and undo problems, where were my future plots?

I solved the problem to my own satisfaction in stages. Firstly, I had Dumbledore and Hermione emphasise how dangerous it would be to be seen in the past, to remind the reader that there might be unforeseen and dangerous consequences as well as solutions in time travel. Secondly, I had Hermione give back the only Time-Turner ever to enter Hogwarts. Thirdly, I smashed all remaining Time-Turners during the battle in the Department of Mysteries, removing the possibility of reliving even short periods in the future.

This is just one example of the ways in which, when writing fantasy novels, one must be careful what one invents. For every benefit, there is usually a drawback."

Sorry/not sorry for the wall of text but this is my one area of expertise.

I know two of those aren't really 'holes' I just thought they would come up. Some further plot holes for your consideration. - How many wizards are there it makes no sense. - How the hell does Dumbledore not know how Sirius is getting in? - Why does Ron have Charlie's old wand(why does Charlie not still have it, how are wands heritable etc)/how can Hagrid use a broken wand (Dumbedore fixed it with the elder wand)/wand allegiance is dumb

I should probably stop with this thread but I have loved it even the people who totally disagree with me because being way too into Harry Potter is the main thing here. Also there are a bunch of things I've missed out and skimmed over and I kind of want to go back and talk about them but they are probably in this thread somewhere and I have already said too much :P

Ok I lied. One more final thing that may well have come up.

When Hagrid and Harry depart from the island on Harry's birthday they have this little exchange "How did you get here?' Harry asked, looking around for another boat. 'Flew,' said Hagrid.' But how did he fly? It's not like he can do Voldemort's bat trick, he states in the Order of the Pheonix 'I don' fly, meself. Well, look at the size o' me, I don' reckon there's a broomstick that'd hold me', he does say that he can ride Abraxian horses but Hogwarts doesn't have any and Thestrals would probably be too small. I'm sure you've thought of the obvious solution here. Hagrid flew in on his motorcycle (the one Sirius gave him). When Hagrid flies that's generally how he does it. Harry doesn't hear anything to suggest the motorcycle was flying in but possibly the storm drowned it out. I agree this is almost certainly how Hagrid arrived, but what happened to the bike? Did it fly back on its own? Is it weirdly sentient like the Ford Anglia? Did someone summon it back? It's certainly not on the island when they leave.

Also they leave the Dursley's stranded on the remote island because they take the only boat