Question: What happened to Hermione's cat Crookshanks? He's not seen at all at the start of this movie. I can't remember if it's mentioned in the books what happened to him; the movie doesn't seem to mention it either.
Answer: The last time we see Crookshanks is at the Weasley house. They likely left him there.
Question: Is there any other way that Hermione could have possibly protected her Muggle parents from Voldemort and his followers besides erasing their memories, like casting a protection spell over them similar to what was done with Harry for the past 17 years or taken them to the Burrow to be protected, or even Grimmauld Place?
Answer: Any of those options would provide some degree of protection, but, should Voldemort ultimately triumph, it's extremely likely that those measures would eventually be circumvented by his forces, leaving her parents entirely at his mercy. By erasing herself entirely from their memories, they cannot be used against her, as they cannot be linked to her (it's reasonable to assume that Hermione would also have arranged for any files linking her to them or that address to be destroyed or altered as well). Erasing their memories also has the side effect of sparing her parents from grief should she fall in the ensuing conflict.
Question: Why did Charity Burbage encourage magical folk to reproduce with Muggles? I know that not all of them hate Muggles, but what did she particularly like about wizards pairing up with them?
Answer: Simple genetics. Wizards staying within the wizarding world are trading the advantage of preserving the wizarding gene for the many disadvantages of breeding within a smaller and smaller genepool.
Question: Why do all of the Death Eaters hesitate to lend Lord Voldemort a wand? In "Chamber of Secrets", when Ron's wand was damaged, Professor McGonagall just said he would need to replace it. So I am assuming that purchasing a new wand is not particularly unusual or difficult.
Answer: Normally replacing a wand is easy, but there are only a few wizards who can make them. Voldemort has kidnapped Mr. Olivander, tortured him, and destroyed his shop, so he is not currently in a position to be making new wands. The Death Eaters fear offering their own wands to Lord Voldemort because he often strikes out, often fatally, at anyone who fails or displeases him. If someone gives him their wand and it does not perform adequately, they know there may be severe repercussions. Voldemort is also gauging his Death Eaters' reaction to his request so he can judge their loyalty and willingness to do his bidding. Most also realize that the request is mostly aimed at Lucius Malfoy, who has fallen from Voldemort's favor. Voldemort is taunting him.
Question: In the movie, the team of snatchers were able to smell Hermione's perfume through the protective spells that she put up. This may seem silly, but why did she have perfume on? It seems quite careless on her part and there was absolutely no reason for her to have it on for their mission, so why the perfume?
Answer: They aren't exactly staying in 4-star hotels and showering every day. Camping is dirty, and with that comes certain odors. And that can get unpleasant in close quarters. It's likely the perfume was her way of countering that. In that instance, sure, her perfume may have been a tip off, but it's not unreasonable to assume that that doesn't come up all that much.
Question: If Dumbledore knew who Tom Riddle/Voldemort really was, then why take him to Hogwarts to teach him magic, since he would eventually grow up to be evil?
Answer: Dumbledore did not know when he first met the young Tom Riddle that he would one day become the evil wizard, Lord Voldemort. He even tells Harry this when they are discussing him. Riddle took the name of Voldemort when he began his rise to power some time after he left Hogwarts. Dumbledore always had suspicions about his behavior while he was a student and kept a close watch on him, but at that time he was unaware of who and what he would become.
Question: In the Ministry of Magic when they try to get to Umbridge's locket, how does she knows that it's Harry? Did she use some magic?
Answer: Umbridge did not know that it was Harry. During the interrogation scene when they are trying to retrieve the locket, Harry is still disguised as Albert Runcorn by the Polyjuice potion. The only thing that Umbridge noticed was that Harry suddenly produced his wand from his coat sleeve. This made Umbridge suspicious and she asked "Albert" what he was doing. That is when the polyjuice potion started to wear off and Harry was transforming back to himself, but he "stupified" Umbridge before she knew exactly what was happening.
Question: At the end when Dobby is stabbed, Harry says he wants Hermione to get something from her bag and she doesn't do anything. Why would she not get anything from her bag. It's unlikely she wouldn't have her bag since she had it at the beginning of Part 2?
Answer: Because she knows that she hasn't got anything in there that'll do any good. Harry's clutching at straws, begging her to pull out something that'll fix Dobby and save his life. She hasn't got anything that'll work, so she doesn't do it.
Question: I don't remember if this is explained in the book, but when it is discovered that Umbridge has the locket, assuming she wore it while she had it, wouldn't she be possessed by its powers like Ron was when he wore it? And did she know it was a piece of Voldemort's soul?
Answer: This was never answered in the book, but in The Muggles' Guide to Harry Potter, it is speculated that Umbridge may have been unaffected because her own evil nature was more aligned to the dark locket. Also, the locket being somewhat sentient may have sensed that she posed no threat to it, whereas Harry, Ron, and Hermione's sole intent was to destroy it.
Question: Why did Hermione clear her parents memory of her at the beginning?
Answer: To protect them from Voldemort. She knows that if he discovers anyone is helping Harry hunt the horcruxes, the Dark Lord will murder their families in retaliation. In the book, Hermione also sent them to Australia under a new identity, and Harry broke off his relationship with Ginny to protect her.
Question: I didn't get it, but who was the "ghost" deer that led Harry to the pond with the Griffindor sword in it? Or why did it lead him there?
Answer: It's not a ghost. It's a patronus, like the one Harry conjured in "The Prisoner of Azkaban," to save Sirius Black. Every wizard's patronus takes a different animal form. An as yet unknown ally (revealed in part 2, and the book) sent the doe patronus to lead Harry to where the Sword of Gryffindor was hidden.
Question: After Harry and Ron find the sword of Gryffindor, how do they find Hermoine again? The camp had enchantments and spells around it to keep them safe and Harry had to leave the protection set up around camp.
Answer: Because Harry already knew where the camp was. The protection spells they use (Harry is shown at one point casting them as well) seem to be sort of like the Secret Keeper spell. IF you cast them or they are cast on you, it allows you to seem through the spells. Also, don't forget that the deluminator led Ron right to the general vicinity of the camp and that the Snatcher team could smell Hermione's perfume through the spells earlier.
Question: How did Grindlewald know that Dumbledore was buried with the wand?
Answer: This is actually never explained in the movie. In the book, Voldemort located Grindelwald in Nurmengard prison so he could learn the whereabouts of the Elder Wand. Grindelwald lied to Voldemort about ever having possessed the Elder Wand, perhaps in a belated effort to protect Dumbledore, his former friend and foe. Voldemort read Grindelwald's mind using Legillimancy and learned that Dumbledore had captured the wand from Grindelwald after defeating him in their epic duel many years before. Voldemort murdered Grindelwald, then deduced that the Elder Wand must have been entombed with Dumbledore.
Question: In the scene where Ginny asks Harry to zip up her dress, George come into the kitchen in the middle of Harry and Ginny's kiss and says "Morning". What is that's sticking out of his ear hole/bandage?
Answer: It's his toothbrush. He's brushing his teeth when he comes into the room, and sticks it in his ear for effect.
Question: When Harry finds the Sword of Godric Gryffindor in the frozen lake, why doesn't he just use the Wingardium Leviosa spell to levitate it out of the lake instead of diving in to get it himself? I assume that this is how J.K. Rowling wrote it in the book, but does this still count as a mistake?
Answer: It is not a mistake. Harry does attempt to summon the sword with a spell, but like the locket horcrux in the sea cave in (in HP and the Half-blood Prince), all the horcruxes, as well as other particularly strong magical objects (like the three Deathly Hallows), are impervious to all types of summoning charms. They therefore must be retrieved by other means.