While Harry is running through Snape's memory a scene from the book is presented. It is about when Snape is still a death eater and listens secretly to the prophecy made by Sybil. However Sybil from Snape's memory is shown making a different prophecy. It is the prophecy made by Sybil in Prisoner of Azkaban. Not only the scene but also the dialogs are wrong.
When Harry and the characters are in Gringotts, they go through a waterfall. After they have fallen out the cart, Hermione gets up, wet, but the next time you see her she is dry (her skin and clothes don't reflect light as much as they did in the previous shot), then in the next shot, she is wet again.
When the trio change clothes after jumping into the black lake, Harry puts on a long sleeved shirt that is gray with a dark collar. Later, in the "limbo" scene, he is shown wearing the same gray shirt with dark collar but short sleeves.
In HPDH Part 1 the entire roof and much of the walls of the upper floor of the Potter home have been destroyed. But when Snape visits after the attack the upper floor is still largely intact. (It is stated in the book that the house has been preserved in the same condition in memory of the Potters.)
In Harry Potter and the Deathly Hallows: Part 1 it was established that the trio had gained control of Bellatrix Lestrange's wand at Malfoy Manor. However in Part 2's Gringotts lobby scene, Hermione-impersonated Bellatrix refuses to show her wand as ID. This was explained in the book that the real Bellatrix had reported her wand stolen and alerted Gringotts prior to the trio's attempted break in. In the movie Griphook can be heard whispering "They know. They know she's an impostor. They've been warned".
It is not explained how Luna Lovegood returned to Hogwarts before Harry, Ron and Hermione. However, many events that happen are unseen, just because we do not see Luna return and do not know her motives, doesn't mean she had none. It is most probable she returned with other members of Dumbledore's Army either to defend Hogwarts or because she thought Harry might return. A deleted scene (appearing in the DVD) shows Luna leaving for Hogwarts shortly after Dobby's death. In the book, Neville contacts the members of D.A. to call them to the Room of Requirement upon Harry's return to the school.
In every film a huge deal is made over the fact that Harry has his mother's eyes. While Geraldine Sommerville, who plays older Lily Potter does have blue eyes like Daniel Radcliffe, Ellie Darcey-Alden, who plays young Lily, has brown eyes.
The goof items below may give away important plot points.
When Bellatrix casts her spell at Ginny in the Great Hall near the end of the film, Ginny is standing in front of her family. However, when Molly Weasley comes forward to attack Bellatrix, Ginny is suddenly behind her father and brothers.
While we are told that Snape conjured the patronus that led Harry to the Sword of Gryffindor in Harry Potter and the Deathly Hallows: Part 1, he had no way of knowing where the trio were camped. This mystery was explained in the book via the medium of Phineas Nigellus' portrait, which Hermione carried in her beaded bag. But Harry had the piece of glass that Sirius gave him in Harry Potter and the Order of the Phoenix, which enabled him to see Aberforth Dumbledore. It is possible that Aberforth recognized the area and contacted Snape.
When Harry is viewing Snape's memory, he sees Dumbledore with Snape, as Snape casts the patronus charm. This is not the same patronus that leads Harry to finding the sword of Gryffindor in Harry Potter and the Deathly Hallows: Part 1, it is merely to highlight to Dumbledore the extent of his love for Lily.
When Lily and James are pictured as they are murdered both in Harry Potter and the Sorcerer's Stone and in Snape's penseive they are wearing different clothing than when Harry uses the Resurrection Stone so that he may have them with him as he dies. The resurrection stone does not always give those brought back the same appearance as when they died.
When Draco returns to his parents (after Voldemort hugs him) he is seen to be leaving in the crowd with Narcissa. In the next shot, he and his mother are still standing in front of the crowd/behind Voldemort. However, Draco and Narcissa didn't actually leave the crowd... they are seen stopping and turning just as the scene cuts to Neville as he is about to step forward. The Malfoys didn't actually leave until Neville pulled the Sword of Gryffindor out of the Sorting Hat and Harry drops from Hagrid's arms, alive.
The first spell (i.e. wand movement) Molly Weasley fires at Bellatrix Lestrange is exactly the same as the second time she fires at Bellatrix (after Bellatrix attacks her and laughs). They re-used the same shot, the only difference is the colour of the spell.