Revealing mistake: When Becky meets Simon in the cube, they hug, then Simon literally stabs Becky in the back. As she falls down to the floor, her black shirt reveals not only some of her chest, but part of a black microphone wire. (01:15:15)
Continuity mistake: When Dr. Doppler and Jim first observe their ship, Dr. Doppler is right next to Jim when he points it out. When the shot changes to a long shot, they're much farther apart. (00:16:55)
Continuity mistake: When Rex strangles Pluto, Dina, who was right by Pluto's side in the close-up, disappears in the side-on shot.
Factual error: It's very nice that the Kate and Jonas clones came out looking exactly like the originals, but the DNA doesn't contain information about the hair length and exact haircut (and mustache, in Jonas' case) at the time of the replication. They would never come out exactly the same.
Factual error: The fake Rheya tries to kill herself by drinking liquid oxygen. The liquid shown is green, viscous, and foaming and looks a bit like the monster's body fluid in Alien. Liquid oxygen is colorless, non-viscous and doesn't produce sticky bubbles. (01:00:25)
Revealing mistake: When the two main characters explode and then implode near the end, you can see that some of the debris being sucked in are passing "through" various other objects, revealing they are computer generated.
Continuity mistake: When Nick Chase first logs into Shock, his password is hidden in the password field as asterisks but when he logs in the second time, he logs in and enters "GUEST" as the password and asterisks do not hide it.
Factual error: When Carl first receives 26 at the hatchery, he asks what kind of dinosaur she is. He is told she is a Hadrosaur (duck-billed dinosaur), but when we see her, she is some sort of Ceratopsian (i.e.: Triceratops). She is later referred to as a Chasmosaur (which while not looking like 26, IS a Ceratopsian).
Revealing mistake: When the doctor intercoms the colonel because he cannot get into the medical room for the pregnant woman having nightmares, the camera shows the intercom, which is simply the back end of a desktop computer with a couple of knobs stuck on it. (00:24:50)
Continuity mistake: There's already drops of blood on the floor and Carrie's hair is already wet before the blood hits her.
Plot hole: Throughout the movie, the flies are vulnerable to light (direct sunlight and even lightbulbs) to the point of incinerating in a split second. Except... they are not; in several sequences they fly to and from bodies and without even taking a direct path (look at all the action happening in front of the house, by the cars, in broad daylight).