In the lunchroom, the amount of liquid in Calvin's thermos cup changes throughout the scene, although he never drinks from it.
Calvin's dad has been gone for 10 years and hasn't aged, which would be possible according to Einstein's theory of relativity if he was traveling near the speed of light, but he says he has experienced 109 years in space and wasn't traveling fast at all, which makes no scientific sense whatsoever.
Comets don't have a tail in deep space so the aliens couldn't have been sampling it for the previous ten years. The tail only appears briefly when the orbit nears the sun due to the solar wind.
Jesper's Comet would have been visible over the entire country, not just a narrow flight path less than two miles wide that Calvin has plotted on his map.
Comets do not move across the sky in mere seconds, they take days to change their position in the sky.
Itsy uses a Microsoft Surface laptop, clearly distinguishable from the logo on the top. Yet it uses some generic Hollywood-operating system with a fictional search engine. It should be running Microsoft Windows and she should possibly use Google or Microsofts own Bing search-engine.
Calvin wants the school authorities to ignore him so they don't discover his legal caregiver has died, but then he draws attention to himself by going to school dressed in a spacesuit.
Obsessively researching Jesper's Comet for 10 years, Calvin doesn't bother getting the original photographs of the comet developed to see if they show evidence of the spacecraft.
Calvin describes himself as an astrologist, but anyone so immersed in the scientific study of the cosmos and aliens would know he was actually an astronomer, not an astrologist (more commonly called an astrologer), someone who deals in superstition, not science.
On finding his missing mother, after searching for 10 years, Calvin doesn't ask her if she knows anything about his missing father, and she doesn't ask Calvin anything about the father's disappearance either, or how Calvin survived when both his parents disappeared.
After arriving at their new house, Itsy and her brother are asked to go over to their neighbor's place and borrow a hammer. Setting out, with a map, Itsy then says "We've been walking for 10 minutes and I haven't seen a single neighbor", yet just before they left home she was watching her neighbor's place through her camera, and it was just a few hundred meters away, as were numerous other houses.
Calvin claims to be an expert on outer space and aliens but says he has never heard of "Star Trek".
Looking up at the night sky, Calvin tells Itsy that "the light from each one of those stars took millions and millions of years to get to us". The light from the stars we can see with the naked eye only took tens, hundreds or thousands of years to reach us. Calvin should know that.