(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.
(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.
The hospital sequence ends with Laurie being cornered by Michael and about to be killed until she wakes up and realizes it was all a dream, one year later. So then how much of the sequence was a dream? Scenes of Michael escaping and Laurie and Annie being operated on are inter-cut together resulting in the sequence making no sense.
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?