(at around 2h) When Hermione stuns Harry to disguise him from the Snatchers, she takes his glasses off him and puts them in her own pocket. When Harry and Ron are put in the cellar at Malfoy Manor, Harry takes his glasses out of his pocket.
(at around 2h) When Bellatrix goes to carve "Mudblood" into Hermione's arm, she moves to Hermione's right arm, in the next shot she's carving into the left arm.
(at around 1h 35 mins) When Harry is preparing to jump into the lake after the sword of Gryffindor, he submerges, wearing his glasses. They are present as he drowns. After returning to the surface, all is blurry and he is no longer wearing them. Harry picks them up off the ice, from a position nowhere near the hole he dove through.
(at around 1h 23 mins) When Hermione first tells Harry of the sign of the Deathly Hallows, the book she had been consulting is lying beside her closed, but in the next shot the book is lying open.
(at around 1h 23 mins) When Hermione and Harry are sitting on the rocks on the cliff the camera behind Harry shows Hermione putting down a book closed, when the cameras switch to behind Hermione it appears that the wind has blown the book open but the cameras switch back to show the book closed again, and switch one final time to see the book yet again open, flapping in the wind.
On the "moving Potter" plan, it is stated that there is one couple on each broom or thestral (one Potter and one protector). Mundungus shares broom with Mad-eye Moody. Shortly after take off Mad-eye passes by Hagrid and Harry and there is no Potter with him. After arrival Bill says that Mundungus disapparated after seeing Voldemort, but when Mad-eye passed Harry, Voldemort hadn't appeared yet, so Mundungus should be disguised as Potter and in the same broom that Mad-eye.
(at around 1h 28 mins) In Harry's flashback of the night his parents were killed, Voldemort is shown in his resurrected form, as opposed to his pre-death state of being. Neither the book nor the movie tell us exactly what Voldemort looked like the night of the Potters' murders. Both, however, allude to his changing appearance becoming less human.
Hermione, when asked by Harry, says she doesn't know how long the Polyjuice potion they're using to infiltrate the Ministry will last. But she had already established in Harry Potter and the Chamber of Secrets that Polyjuice potion lasts for exactly one hour. JK Rowling has stated that how long the potion lasts varies depending on how well it's brewed.
(at around 1 min) When Hermione first appears in the movie she has a newspaper. The picture of the Muggle family does not move even though it is in a Wizard newspaper. However, one must assume that because it is, in fact, a Muggle family that they would not have had a Wizard picture taken of themselves, and the picture is a Muggle picture, hence the subjects' stationary positions. It can be seen that the headline picture, however, does move.
During Harry Potter and the Chamber of Secrets (2002) Hermione states that it takes at least a month to brew a batch of Polyjuice potion. However, Harry, Hermione, and Ron seem to have brewed up a batch virtually overnight when they infiltrated the Ministry of Magic. In the book, it was stated that Hermione obtained a supply of Polyjuice Potion from Mad-Eye Moody's private stores.
Anyone that wears glasses on a daily basis would remove their glasses when preparing to dive into water (at about 1:35). This depends entirely on how bad their eyesight actually is. It is established multiple times in both the books and movies that Harry's eyesight is really terrible without his glasses and if he'd have removed them before diving into the pond he wouldn't have been able to see the sword.
When Fred and George appear at the Burrow after being chased by the Death Eaters, their shorter "Harry" clothes still fit them.
It's obvious that Harry's glasses don't have lenses during certain parts of the film.
(at around 1h 30 mins) When Hermione is reading Rita Skeeter's book, she tells Harry that she has discovered that the boy in the photo at Bathilda Bagshot's house is Gellert Grindelwald. When she hands Harry the book, if you look closely, you can see there is an oval shaped hole in the front cover where the moving picture of Dumbledore would be.
(at around 14 mins) After Fleur transforms into a replica of Harry she (as Harry) is seen standing with her shirt off wearing a bra. The bra's cup size is far too small and positioned far too high on her chest to have been worn while Fleur was still herself.
Nagini is a python. When Voldemort allows her to eat the human teacher (Charity Burbage), it would take three weeks to fully digest. In the next scene with the snake, there is no sign of having eaten a whole human, which was a week after eating.
When Harry and Hermione dance, the song 'O Children' by Nick Cave and the Bad Seeds plays on the radio. However, this song was written in 2004, whereas the film is set in 1997.
(at around 1h 7 mins) Just after Harry and Hermione fail to destroy the Horcrux and Harry says "We need to keep it safe", he looks inside the piece of his mirror, the camera is briefly seen in the reflection.
When Harry and Hermione leave Godric's Hollow via apparition, the window they're standing by explodes and shatters. The film holds on this shot for a few seconds. During that time smoke is pouring out of the window. That smoke would not have been caused by Harry and Hermione at all. It is actually coming from whatever air cannon or device that was used to destroy the window. The editor leaving it in is a very strange inclusion.
Harry and Hagrid leave the Dursleys' home in Surrey to head to the Burrow, which is supposed to be in Devon. They should be flying west, but have an encounter with Death Eaters at the Dartford Crossing. This means they have inexplicably flown east instead.
When Harry, Ron and Hermione are spotted by the Snatchers after apparating from the Lovegood House, why do they run, rather than joining hands and apparating elsewhere?
When the look-a-like Harrys and their partners arrive in The Burrow, Lupin tests Harry, to ensure that he's the real one. As the others start arriving, Kingsley Shacklebolt tests Lupin, but Lupin does not test him back. No other people are tested.
Since Yaxley, a Death Eater, saw the trio during the Ministry escape, there should be no identification needed later at Malfoy Manor. Ron and Hermione are, by that point, known to be with Harry.
Harry has a broken shard of a mirror which he says he got from Sirius, but Sirius is never shown giving it to him.
Voldemort insists on killing Harry himself multiple times throughout the series. He also has a direct control over Nagini, as the snake is a Horcrux. Therefore, Nagini should never attack Harry, as Voldemort never hinted that a bite from his pet snake would suffice.
When George and Fred are talking to Harry in the Dursleys' house, the twins go from being in the back of the room to the front. Although these characters have been shown to be fond of Apparating short distances, at that point in the film, the house had had an anti-Apparation ward placed over it to prevent Harry from escaping the Death Eaters unnoticed.
Throughout the books and movies, Harry Potter characters only ever use quills to write. When drawing the Deathly Hallows symbol, however, Xenophilius Lovegood says repeatedly "I need to get a pen." He repeats the word "pen" several times and then proceeds to draw the symbol. Though it's hard to see what tool he is using to draw, he is clearly not using a quill.
Dobby tells Ron that it is good to see him again. In the context of the films, Dobby and Ron have never met. This is a holdover from the books in which Dobby has a much bigger role. Either no one caught this, or it was left in to try to insinuate that the trio in the films are very close to Dobby.
Before leaving Privet Drive, Mad-Eye says "Head to the Burrows". This is repeated in Harry's flashback. The Weasley home is actually called The Burrow.