Plot hole: Why is that shark machine even there? The only reason it's there is to help the plot, and I don't see how it is of use to anyone in the corporate world. If the shark just ejects the fish it turns into fish heads out to sea, there is too much chance they will be ruined by carnivorous fish or weather before they are picked up. And fishing companies should know better.
Plot hole: There is a scene setting up the nonsensical resolution of the plot, when the policeman recaps the various baby sightings. First; he already got 'fake' reports he chased, there was a scene about that, let's ignore the fact that certainly he would have gotten more like that and he conveniently for the plot lists just the few relevant ones. Second; the baby was kidnapped at 10 and the baby sighting on the bus happens "in the morning." Then the zoo sighting happens "at 3 o'clock." The construction site closes at 5 o'clock. Even forgetting the superior stamina of the 9 months baby that has been walking a whole day without a break, that's a lot of stretch for the actions as shown in the movie, in particular the time between the bus and the zoo; the bad guys would have been loitering in search of the baby for hours between the bus incident and the moment when he leaves the department store to get to the zoo.
Plot hole: At the very beginning, as the passenger ship is foundering in a powerful storm, the little boy places his kitten in a box and tucks the box inside his shirt just moments before he is cast into the churning sea. Sinking into the depths, the boy and other passengers are presently rescued by Captain Nemo's team of divers, who supply the drowning passengers with oxygen until they board the submarine Nautilus. Once aboard, the little boy opens his hidden box to reveal a wet but very much alive kitten that could not possibly have survived submersion for that length of time in a box that was not waterproof.
Plot hole: Even if Chicken Little was tagged out when he hit home plate, the game was already tied so his team would still have a chance to win the pennant.
Plot hole: In the first film, the shape of the ring was a little different and it was set in a ring. Also, it was given to Xania. In the second film, she was never even acknowledged as donating it to the museum.
Plot hole: Mr. Cranston asks Denise to be the accompanist for the school's production of "Chicago". This is an error. In the year 2009, in which the film is set, this would be impossible since the licensing company which has the theatrical rights for "Chicago" restricts the show from being produced (even by amateur groups and schools) anywhere in the greater New York area while there is an open-ended production running on Broadway.
Plot hole: In the series we learn that these creatures take a lot longer than us humans to grow up and that they live a lot longer. They mention that the children are about 900 years old, so a grown-up would be more than 1000 (probably 2000). The series is set around our time (1990s/2000s) and Fjellrose and Erke are very old. Yet the film is set about 100 or 200 years ago, you can tell by the way the humans are dressed and the way their houses are built etc. So Fjellrose and Erke should still be grown up, but they are young children. If they are only 100 to 200 years younger, then they should be much older in the film or much younger in the series.
Plot hole: Eagle catches and flies off with one of the cubs and Benji goes chasing after the eagle. After a bit of searching he spots what appears to be the missing cub but then Benji is chased by the nearby eagle before turning around to drive it off. But strangely Benji abandons looking for the fourth cub, as from this point forward we only see three cubs with him. This doesn't jive, as Benji has up to this point done everything to protect the cubs and keep all four of them together. (00:58:20 - 01:00:06)
Plot hole: When Dubois attempts to kidnap Alex using the tranquilizer, she is brought to a halt by several different zoo staff thanking her for returning him. The entire first movie's plot is based on them being stranded on Madagascar after being on a ship that was intended to take them away. The actions of the animals at the train station were on the news, and a large gathering of sorts was held to show that the animals were leaving the zoo. Therefore, no one should have reacted this way to his return.
Plot hole: If Chester's plan was to steal the machine the entire time why didn't he just have his people steal the machine while it was still floating in the air during the first film? There was plenty of time to capture it before the food started mutating so what was he waiting for if he needed it so bad?
Suggested correction: Because he wasn't there in the first film? He first made an appearance in this film, doesn't know how to work the machine without Flint, and how the hell would he even get it in the sky? He also didn't even know about it, or what happened to Chew and Swallow, again, until he made an appearance in this film. Not a mistake.
Plot hole: Emily begins to pull Henry out of the shed, but however there is no track leading to the other end. Also, the turntable is not big enough for both engines to fit on.
Plot hole: Since the criminals who used the dogs to rob the bank in the first movie were never apprehended (No criminal worth their salt would tell the authorities their caper was spoiled because the canines ran off with their loot), there is no way the people who are hunting the dobermans in the beginning of this movie would know the dogs were still carrying the cash. (00:18:00)
Plot hole: Gail and Katie talk in her shed about Guy's phone call. Katie says "I didn't lie about anything", which is a really odd non sequitur. All Gail said was "I just got off the phone with Guy Morgan. Your phone. He just loved that little demo you left him. I have underestimated you. It'd make me proud if I actually cared about you." Nothing about it prompts a response like that, except the plot point that Gail told Guy that Katie lied about it appropriating Bev's demo. But Katie does not know that fact at that point. (00:21:00)