(At around one hour and forty minutes) According to Tom Felton, Voldemort awkwardly hugging Draco was not scripted, but an improvisation by Ralph Fiennes. Felton's reactions of stopping dead in his tracks, not knowing what to do, is genuine.
(At around thirty-seven minutes) The fight between Professor McGonagall (Dame Maggie Smith) and Professor Snape (Alan Rickman) was considered to be changed into Harry (Daniel Radcliffe) against Snape instead. The idea was scrapped by J.K. Rowling, who insisted that the duel should involve the same characters as in the novel, as she saw it as a key moment for McGonagall.
In every shot in which Voldemort (Ralph Fiennes) and Bellatrix Lestrange (Helena Bonham Carter) appeared together, she always moved so that she stands on his right, traditionally the position of the most loyal and trusted follower.
(At around fifty-seven minutes) When Harry goes into the Room of Requirement, in the bottom left hand corner, there is the knight that Ron rides from Harry Potter and the Sorcerer's/Philosopher's Stone (2001). Also present are the Cornish Pixies set loose by Gilderoy Lockhart in Harry Potter and the Chamber of Secrets (2002). The set is made entirely out of props from all of the movies, around seventy-two containers of props.
When Harry, Ron, and Hermione enter Gringotts near the beginning, Hermione has taken Polyjuice Potion to disguise herself as Bellatrix. Before the scene was shot, Emma Watson acted out the scene for Helena Bonham Carter so she would know how to act as if she were Hermione in this situation. So, essentially, this scene is Carter acting like Watson who is acting like Hermione acting like Bellatrix.
Sean Biggerstaff: (At around one hour and five minutes) Biggerstaff's character, former Gryffindor Quidditch Captain and Keeper, Oliver Wood, leads an aerial assault on the Death Eaters via broomstick during the Battle of Hogwarts. He can clearly be heard saying, "Come on!" to six people, also on broomsticks.