Plot hole: During the scene where Merida gives her speech on "breaking tradition", her mother, as a bear, moves silently behind the majority of the crowd, so they don't see her. Fair enough. However, Merida and her father's clan are all looking in the same general direction (towards the crowd) while she's speaking - how does no one from Merida's clan see a bear moving at the back of the room?
Plot hole: Frankie makes reference to fear of fire early in the movie in the scene with all the guests arriving at the hotel. And in the scene in the local village with the monster festival, a single match is used to send him on a rampage. But throughout scenes in the hotel itself, there are lit candles, candelabras and torches throughout, most noticeably in Mavis' room during the scene where her monster friends (Frankie included) are addressing her idea of going to a human village. None of this fire affects Frankie at all.
Suggested correction: Candles are a controlled fire, and small in a room that's mostly made of stone. The match at the town was a sudden fire in front of his face that startled him. Even if he was concerned by the candles in the past, I'm sure that in the 115 years since the hotel opened, he was OK with it.
Plot hole: When Dex is rescuing the baby kittens from the Fat Cat Burglar on the hot air balloon, whilst it is flying over the city, the four hairless hamster henchmen fly off the balloon and plummet down onto the street. Dex then saves the baby kittens and lands in the park, where two of the henchmen are shown landing in the park after plummeting. Three problems with this. 1) The henchmen fell before Dex saved the kittens and made his way down to the park, so how did they land on the ground long after Dex landed on the ground? 2) How did they land in the park if they plummeted from above a street? 3) How are there only two henchmen shown landing when four of them were shown falling all at once? (00:04:30)
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.