When Wilbur throws Lewis off the roof onto the invisible time machine, Lewis falls flat onto the glass dome, complete with hollow glass dome sound effects. When the time machine becomes visible however, the dome was already open and Lewis actually fell onto a chair. His limbs should have stopped falling at different levels than his torso.
During the T-rex attack, the train and pizza dough disappear after they are used against the dinosaur.
After Mildred schedules the interview for Lewis, she is holding the phone in her left hand. After Goob replaces the coffee in her right hand with his juice box, she turns into Lewis's room. The juice box is still in her hand but the phone has disappeared.
When the time machine crashes, Wilbur is seen holding onto the steering wheel of the time machine, clearly detached from the time machine. At the next scene, when Lewis and Wilbur are looking at the damage done to the time machine, it can be seen that the steering wheel is intact with the time machine.
During the 'pop quiz' scene, where Wilbur is asking Lewis about all he knows about the Robinsons, Lewis refers to Wilbur's dad as 'your dad, Cornelius'. He does not meet Cornelius before this point and no one told him Wilbur's dad's name, yet he knew anyway.
Fire sprinklers don't work as depicted in the gymnasium scene. They are set off by heat (flames) not just smoke, and only the affected sprinkler releases water, not every sprinkler in the room or building.
The meeting where the Bowler Hat Guy passes off his invention as his own takes 1 minute and 44 seconds instead of two minutes.
Wilbur picks up Lewis in his flying car time machine to visit the futuristic city. First of all Wilbur would have likely disappeared since Lewis is his dad who changed his name to Cornelius and would not have been able to marry his future wife Franny Robinson to have their son Wilbur and Franny would have been single or married a different boyfriend. Also, it would not be possible for the younger Lewis to meet his older self since he would also disappear. Also, many of the inventions Lewis made for the utopia society including the Doris robot hat would have likely disappeared and not get invented since Lewis is not there to make it happen.
When the Bowler Hat Guy is trying to pass off the memory scanner as his own, he is seen carrying the memory scanner in the box right side up, and then after the introduction is seen taking the box off the top, but in order to do that, either the box would have had to have been turned upside down, or the bottom would have had to been loose, in which case the memory scanner would have fallen out.
When Lewis is exiting Jake's Electronic Store with his wagon full of parts, the window on the left has a typo consisting of "Computers T.V.s VCR CD/DVD STERIO", stereo is misspelled.
The gym teacher should have had severe cuts on his arms due to broken glass rolling off of them.
The science fair takes place at an elementary school. Lewis had stated to Mildred that he is going to be 13 in the coming year. This would place him in middle school, not elementary school.
When the Bowler Hat Guy is explaining that Doris was designed to be a slave to humankind and she attacks the scientist is the first time Lewis is unknowingly seen as an adult.
When Franny is asking Wilbur "What does he mean by if he had a family?" When Wilbur responds he has a much younger sounding voice then a few seconds later his voice is deeper again.
When Lewis is being chased by the Doris building, as he is attacked by the normal size bowler hats, the building turns to (perspective) Lewis' right. After going through the tunnel, the building has cut him off, but has come from Lewis' left side.
When Michael "Goob" Yagoobian known as The Bowler Hat Guy steals the blue flying car time machine for his schemes to change history, it is never found or recovered and it is unknown where the flying car time machine was abandoned at, since the film never explains what became of the abandoned stolen time machine Michael stole which is likely in Lewis' present time.
The whole evil Doris scheme and the theft of the memory machine were carried out by the adult Goob who wanted revenge because he had fallen asleep as a child and missed catching the baseball. However, when Lewis woke him up and he caught the ball that changed everything and he no longer would want revenge so he would never have time traveled in the first place.
Despite attending the same school as children, Franny fails to recognize young Lewis when he comes to the future. This is explained away for Bud and Lucille as they appear to have memory issues but Franny has no reason to not remember her husband as a child.
When Lewis is explaining how the memory scanner works, he says that memories are stored in the cerebral cortex. They are actually stored in the limbic system and temporal lobe.
Franny's reason for trying to remove Lewis' hat is a "no hats at the dinner table" rule. However, several members of the family--Billie, Laszlo and Tallulah, and Art--wear hats as part of their outfits, and none of them are asked to remove their hats before sitting down.
Mr. Harrington should have been taken to a hospital and remained there for four to six hours after being injected with epinephrine, since he was accidentally squirted by Lewis' peanut butter and jelly invention. Mildred also never mentions to Lewis that Mr. Harrington was taken to a hospital after she called to check on him.
At the science fair Dr. Krunklehorn explains that her invention, the Caffeine Patch, has 12 cups of coffee per patch and shows she has 16 visible patches on her right arm. That's 192 cups or 12 gallons of coffee.
When Bud and Lewis enter the bathroom, they do not plug their noses. However, when Wilbur enters the bathroom, he plugs his nose.