In the opening battle scene, Jeb's HUD displays a "System Overload" warning after he was shot by the Sedition raider. That warning was actually displaying since the moment he launched. It also disappears right after Don moves in to rescue him.
While running away from the spiders on the Proteus, Major West trips twice.
When the robot is removing the restraining bolt, a close-up shot shows him using his left arm. The long shot of the robot removing the bolt shows all his arms (including the left one) waving about in the air.
When Penny is talking to Will about jettisoning his body into space, the package in her hand suddenly disappears when she claps her hands together. Immediately afterwards, she retrieves it from her left.
After Penny opens the package containing the ladder she escapes with, she stands up. The package is in her left hand by her knees, and her right hand is down at her side. In the next shot, she's cradling the package in her right hand up at her waist.
As the Jupiter I is lifting off from Houston, the pyrotechnics used to simulate the rocket motor blast actually causes the entire top half of the ship model to jump up and separate from the lower half briefly.
In the opening shot pulling out to reveal the Hypergate, one of the CGI vehicles moving around the structure flies through a solid part of the Hypergate.
After everybody is cryogenically frozen, the pods are moved up behind windows. When the pods halt, the person in the right-most pod moves his/her hands. They should be frozen solid and unable to move.
When Dr. Robinson analyzes the spider, only its image appears on the screen, but she already knows its a silicone-based life form, even though this information does not show on the monitor yet.
Right before Penny shorts the power to the cryo pod, Smith can be seen with his crowbar firmly in the door seal, Immediately after the power is shorted his pry bar is no longer in the door but Maureen effortlessly opens it.
When Dr Smith is talking to the Global Sedition Man in the Holo-Desert. He screams "Where is my money". The next shot is a close-up of his face and he has his mouth wide open, yet he still manages to say nearly a whole sentence without moving his mouth.
When the spiders are about to break through the door on the Proteus, a shot from the robot's point-of-view shows John Robinson saying "Will, we have to get that door open," a few seconds before his mouth moves.
After Major West falls over startled from the spiders behind him, you see him take aim to shoot the spider on his chest. In the next shot, you see the flare from the gun firing, but there's no sound. Two shots later he fires the gun, and it functions properly.
During the attempted destruction of the Jupiter, there's a brief moment (right after Major West gets blown back by the electric blast) where you hear the robot's pulse blaster firing, but don't see a beam.