Plot hole: Following Glen's death, Nancy tells her father to come across the street in 20 minutes to catch Freddy. She then goes to her house, checks and sets her alarm clock, and proceeds to rig the entire house with booby traps, including filling a light bulb with the contents of several shotgun shells, and has a heart-to-heart talk with her inebriated mom. When she gets back to her room to go to sleep, she checks her clock again. The time on the clock has advanced only ten minutes, not nearly long enough for everything she did.
Plot hole: When the doctors are discussing the condition of Bowman's mother, a newspaper headline on the wall displays the pictures of both Bowman and Frank Poole. These pictures are actually still shots of the two actors from an earlier conversation they had with HAL in the previous film. Since Discovery has been dormant for nine years, how did Earth manage to use these particular shots for the newspaper?
Plot hole: When Arnie is driving the cop car and shooting at Conner and Reese, 5 or 6 inch holes from the gunfire are shown in the door right beside Connor. If the shell penetrated the steel door (which it could easily do - and was shown to do), there's nothing inside the door or on the other side of it to stop the bullet. Connor, and probably Reese, would've been ripped to shreds.
Plot hole: Billy's not tall enough to impale Linnea Quigley on deer antlers.
Suggested correction: The movie blatantly shows Billy lifting her high enough above his head to impale her. It's literally right there in the scene. Additionally Linnea Quigley talks about the making of the scene in the documentary "In Search of Darkness Part II," and talks about the actor living her high above his head over and over while making the scene.