Factual error: When the Jupiter 2 blasts off, it does so in the most fuel inefficient way possible - flat surface first. The air resistance would be fifty times less if they'd angled it side on. Plus, when the aerodynamic cover blasts away, the Jupiter 2 itself is revealed - and it is more aerodynamic than the cover. Rocket science must have taken a few steps backward lately... .

Continuity: When Penny is sliding down the rope to get the microsealer, she knocks the silver device to the edge of the toolbox. In the subsequent closeup, the silver thing is back in its original place.

Revealing: During the attack of the Global Sedition on the space station at the beginning of the film, several objects can be seen with dark grey boxes around them - CGI artifacts. One clear time is when Ranger 1 is saying "Damn, can't shake him".

Continuity: When Dr. Smith is attempting to resuscitate Penny, she is strapped to the bed. Yet when they make the jump into hyperspace, she is suddenly unstrapped and floating.

Revealing: When Penny and Blart are reunited at the end, the animators didn't put the creature where Penny is looking. She also tries to lift it onto her shoulder, but it is nowhere near her hand.

Plot hole: Considering that this family has been training for the mission for years and certainly have received some instruction in astrobiology, they are awfully carefree around the cute little alien. Any real space farer would be aware of the enormous potential problems with first contact, like incompatible biochemistry (aliens might exude deadly toxins from their skin, be eaten alive by human-exhaled oxygen, etc). They even feed it human food without analyzing the alien; again, this could kill it, make it chemically dependent, cause it to go into a mating cycle, etc. But it's cute alien, so naturally they don't worry about any of this.