I think there are some possible contradictions or areas that never got fully explained (imperious curse, for one), but I don't think they are huge, huge plot holes.
And perhaps what is unknown now shall be revealed in this Harry Potter encyclopedia JKR has been talking about.
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well here is a small example. she wrote that harry had the "real" invisible cloak that was impenetrable, truly invisible and what not, yet mad eye could see them through it. there are others too but does anyone have an explanation for that
I don't recall any contradictions with the Imperius Curse.
However, there was a rather huge one with the Fidelius Charm - in earlier books it was explained that even if the Secret-Keeper died, the charm was still in place. In DH though they say that since Dumbledore (Secret-Keeper for Grimmauld Place) died, everyone who knew of it became a Secret-Keeper which weakened the charm.
I don't think the charm was weakened in terms of magic, but the fact that there were numerous secret keepers who could give away it's location (e.g. Snape) thereby defeating the whole point of the charm's existence
There wasn't numerous Secret-Keepers, though. There was only one - Dumbledore. Knowing where something or someone protected by the Fidelius Charm is doesn't make you a Secret-Keeper.
Wasn't Dumbledore also able to see through the cloak when he found Harry looking at the mirror? Also, Snape seemed to sense Harry closed to him when he was confronting Quirrel in Sorcerer's Stone.
One thing I didn't like was Ollivander's explanation as to why Harry's wand acted on it's own against Voldemort. It didn't seem to make a lot of sense to me.
Harry wasn't wearing the cloak when he was looking at the mirror, he had taken it off.
And I don't think turning invisible will make all hints of your presence completely disappear. Otherwise they wouldn't have to worry about not making noise or bumping into people.
Well okay here's the biggest contradiction I think. You know how the outer part of the horcrux has to die or be broken for the horcrux to be destroyed. Well Harry didn't really die so the horcrux shouldn't have been destroyed. And besides Voldemort shouldn't have even been able to kill Harry even if Harry was accepting death because he had the blood protection off harry's mom in him which Dumbledore said as long as it was in Voldemort, Harry couldn't be killed by him. But the thing is that protection would and should have gone away after Harry's 17th birthday like it did with Harry.
No, Voldemort couldn't kill harry not due to the protecion given to him by his mother's sacrifice, but because Voldemort had the same blood as Harry's running through his body, therefore there was something tieing Harry to the living world. So as long as Voldemort was still alvie Harry could not die.