(at around 42 mins) During Loomis's interview in front of the dilapidated Myer's house it is obviously not the same house used in the previous film.
(at around 16 mins) In the opening hospital chase, the bandage on Laurie's head alternates between blood soaked and clean between shots.
(at around 55 mins) When Loomis is doing the book signing before the guy comes at him with the gun he signs the book with a black pen, this changes to red in the next camera shot.
(at around 2 mins) The shirt that Laurie wore in the beginning of the film when she's walking with the gun and being pulled through the hospital, it's obviously not the same shirt used in the first movie.
(at around 1h 17 mins) When Laurie and Mya find Annie near death upstairs, Laurie tells Mya to go and call the police. Mya agrees, and slowly walks off screen, as Laurie turns away. The next shot shows Mya sprinting from that spot, with Laurie completely out of sight, not even standing in the door frame. But in the shot after, Laurie is clearly standing in the door frame, which was completely visible in the previous shot.
During the book signing, Lynda's father tells Dr. Loomis that Michael butchered her, but in actuality he strangled her.
(at around 7 mins) When Coroner Hooks and Gary Scott have a car accident, you can pause a few frames before the crash, and clearly see that a small explosive detonates in-front of the bumper before they hit the cow.
The Rob Zombie iterations of Halloween clearly remove any supernatural aspect from the character of Michael Myers, this results in a plot inconsistency from the first film. It is never explained how Michael was able to survive a gunshot wound to the face at point-blank range without immediate medical attention.
In this film, both Laurie and Michael start seeing visions of their dead mother and a younger Michael. Laurie could not possibly envision Deborah or a younger Michael because she never met either of them at that point in their lives. Also, it seems odd that Michael is experiencing these visions now and never happened in the first film.
(at around 46 mins) It is vaguely mentioned that Michael's body was misplaced by the police from transport from the crime scene to the morgue. This appeared to happen in the outskirts of Haddonfield. So why did it take a year for Michael to return to the town to find Laurie?
The doctors at the hospital perform surgery on Laurie without cleaning any of the gore off of her. One of the steps in surgery is to do a full wash of the body.
Actress Caroline Williams, who plays Dr. Maple, accidentally refers to Nurse Daniels as Octavia at one point (the actress is named Octavia Spencer in real life). Actors can play characters with the same first name so it's obvious Nurse Daniels' first name is Octavia.
During the hospital scene, when Laurie goes to Annie's room and cries for her begs her not to die. Annie is supposed to be unconscious (or in a coma) but when Laurie touches her face, Annie can be seen flinching.