Continuity mistake: In the dormitory, when lovestruck Ron is going gaga over Romilda, he is wearing a brown sleeveless tee shirt and its tan trim has many holes. When Harry brings Ron to Slughorn, Ron is still wearing that tee shirt, but now some of the holes are gone and the rest of the holes have changed position. (01:26:50)
Revealing mistake: It is not what is seen here that is the problem, but what we don't see on the Hogwarts Express; first on the way to Hogwarts when Harry, Ron, and Hermione are in their compartment talking about Draco, and second, during holiday break, when Harry and Ron are talking about Unbreakable Vows. As the camera faces the large compartment window, we see the scenery out the window, but as the train speeds along, the scenic reflection of the windows opposite it, in the corridor, should be seen but isn't. What is reflected is the light colored wall of the compartment beneath the blacked-out window. The camera filming the shots from this angle is positioned at that window, and to hide the camera/crews' outline, the window was covered.
Continuity mistake: In Potions class, when Hermione stands before the cauldron explaining what she is smelling in her closeup, we see Neville behind her with the broad space to his right (viewer's left), just as she says, "Spearmint toothpaste". In the instant cut to the wideshot, Harry is now shoulder to shoulder with Neville, too fast for him to suddenly be standing that close to Neville. (00:34:35)
Continuity mistake: When Harry is kneeling beside Dumbledore's body, at the foot of the Astronomy Tower, Ginny joins Harry and holds him at his left side (viewer's right). In the last close-up of Professor Dumbledore's face, Harry is visible in the background with a space to his left and Ginny is now gone. That same angle was shown before Ginny joined Harry.
Continuity mistake: When Hagrid and Slughorn are drinking after Aragog's funeral, Slughorn's cup is considerably larger than Hagrid's (an effort to show size difference between Slughorn and Hagrid), and note when Slughorn holds his cup how large it is compared to his hand. But after Hagrid passes out Slughorn's cup is now the same size as Hagrid's cup - Slughorn's hand is resting on the table right beside the cup, which is now significantly smaller compared to Slughorn's hand. (01:50:05)
Visible crew/equipment: At the end of the Quidditch match, when Ron shouts, "Woo hoo!" with his arms raised, just as his cape flaps around the black seat on the actor's broom becomes visible. There are a couple of other quick glimpses of a seat during the Quidditch match. (01:38:45)
Other mistake: In quite a few shots during the film, it is much too obvious that there are no lenses in Harry's glasses, whereas in previous and following shots the glasses have lenses. A couple of instances are: when Harry drinks the Felix Felicis and when Harry kneels beside Dumbledore, at the foot of the Astronomy Tower.
Continuity mistake: When Harry and Dumbledore return from the Horcrux cave, Dumbledore sits down with his arm around Harry's neck. When Dumbledore asks Harry to go fetch Snape, his arm suddenly disappears, and there was no time for him to have moved it. (02:10:00)
Revealing mistake: Immediately after Katie is cursed by the necklace, Harry, Ron and Hermione are in Mcgonagall's office talking about what they saw in Hogsmeade. Harry says, "It was Malfoy." As both teachers turn Mcgonagall says,"That is a very serious accusation, Potter." As she says this, she looks oddly transparent. You can see the window pane design through her robes, particularly in the shoulder. This continues to be true until she says "I suggest you go back to your dormitories." This could possibly signify a green or blue screen behind them. (00:54:10 - 00:54:40)
Continuity mistake: When Harry, Ron and Hermione are at the Three Broomsticks talking with Slughorn, Slughorn spills his butterbeer on Hermione and the table. Still in the conversation, the table is shown, but it's dry. Then a little later, there is foam on the table but only near Harry's glass. The rest of the table is still dry.
Continuity mistake: In the dormitory, when Harry walks in to see lovestruck Ron at the window, Romilda's card and empty chocolate wrappers are on Harry's bed. When Harry places the Marauders map and Potions book on the dresser, the card and wrappers have changed position. (01:26:55)
Visible crew/equipment: When Slughorn stands before Tom Riddle speaking of seven Horcruxes, as the professor faces the fireplace and says, "This is all hypothetical," and when Tom replies, "It'll be our little secret," in these close-ups particularly the square lighting/reflector screen becomes clearly reflected in their eyes.
Continuity mistake: At the Three Broomsticks, when Slughorn spills the drink the foam by his fingers disappears, reappears, disappears, and so on.
Revealing mistake: During Quidditch tryouts, when Ron blocks the Quaffle with his head in the closeup, Ron's body disappears at the bottom of the screen below the digital editing line. (Only visible on fullscreen DVD).
Continuity mistake: When Slughorn and Harry are talking at The Three Broomsticks, Slughorn's grip on the silver mug repeatedly changes. His fingers are either at the top of the mug or at its center, depending on the camera angle.
Continuity mistake: In the living room at the Weasleys' house, while Harry, Arthur, Nymphadora and Lupin are talking, in the shot facing Lupin, Harry's shoelace is untied. After a brief cut to a shot facing Nymphadora and Arthur (where we can see Harry's hands), it cuts back to the original angle and now the shoelace is tied. (This has nothing to do with Ginny tying Harry's shoelace much later on.)
Continuity mistake: In the scene with Weasley's Wizarding Wheezes, as the camera pans up the front of the store, one sees the store name (in gold lettering). However, when Harry, Ron, and Hermione leave the store to follow Draco Malfoy the store name is no longer present.
Continuity mistake: Near the start, when Slughorn shows Harry the framed photographs, the frames change position between the wideshot and close-ups.
Continuity mistake: During dessert at Slughorn's supper party, the napkins that hang from some (Belby, Neville, etc) of their collars change positions in consecutive shots. (00:56:50)
Continuity mistake: After Harry arrives at the Burrow, when he, Hermione and Ron are sitting and chatting, Hermione changes position - notably her knee is up, down, up, etc.
Suggested correction: She's not transparent. It's a trick of the camera. A glare from the bright window behind her. You notice you can't see the vertical slats of the windowpane. Only the horizontal. That's because the glare is carrying across her body horizontally and where the horizontal slats are there's no light to cause a glare.
I can see the horizontal and vertical ones through both McGonagall and Snape. I can even see the desk through the middle of her body.