(at around 59 mins) In the bathroom scene where Cleveland Heep is speaking with Story, you can see a towel rack directly behind him with two towels hanging on it. They are both draped on it with the same length of towel showing. In the subsequent scene when they pan back to Cleveland, the towel on the right is clearly shorter than the towel placed on the towel rack on the left.
(at around 1h 4 mins) Given the length of the words mentioned, 9-across cannot touch 27-down in a crossword puzzle, as Mr. Dury says interpreting the puzzle while Story is in the shower (it would have to be at least 19 letters long to do so).
(at around 4 mins) When Mr. Heep introduces Mr. Farber to Young-Soon Choi, he tells him that she lives down in apartment 8A. However, later on (at around 21 mins) when Mr. Heep goes to see Young-Soon and her mother the number on the door says 16B.
Before Cleveland Heep dives into the pool after Story, he takes his glasses off. After Story saves him, his glasses appear and disappear during shots, especially during the sequence where he is talking to the tenants.
(at around 1h 16 mins) At the pool party the overhead view shows the flood lights facing the lawn. When Anna is taking her place, she takes off her sweater because the flood lights are facing the pool. Later they are facing the lawn again.
(at around 13 mins) In the apartment just after Cleveland rescues Story, we see Story talking to Cleveland. From Story's perspective she is looking directly over her knees which are closed towards Cleveland. It would appear she is sitting normally on the sofa. From Clevelands perspective, she is looking to the right of her slightly apart knees, and sitting length-ways on the sofa.
(at around 1h 23 mins) The Scrunt drags Story though the mud and grass grass during the attack. Story just has scratches on her legs even though she was dragged by her arm. Her arm appears to be uninjured. Her shirt shows no signs of mud, blood, or grass stains after the attack.
(at around 32 mins) When he sees Vick's book "The Cookbook," Cleveland Heep says to himself, "This is s-s-s-s-silly." Stutterers often do not have a stammer when talking to themselves; they stutter primarily when talking to other people. However, Cleveland's stutter is a symptom of Post-traumatic Stress, in which case the stutter typically remains constant regardless of social situation until the stress is dealt with.
(at around 57 mins) Story says that she is forbidden to talk about her blue world to humans and therefore communicates with sign language when talking about her world yet she tells Cleveland everything he needs to know about how to spot a scrunt in grass through a walkie-talkie.
The Tartutic creatures punish the scrunts if they are to break the rules of the blue world. These rules are never established or laid out so we don't know what rules the scrunt is breaking, and if these creatures are so evil then why would they care about who's being fair?
The goof item below may give away important plot points.
(at around 1h 35 mins) When the Scrunt is trapped in the apartment building hallway during the departure ceremony, it paws and pounds at the door to escape and attack Story. When it finally breaks open the door, the door jamb splits open. However, as the Scrunt escapes we see that the door opens inward, not outward.