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: According to the phone book the name given was "M. Horowitz" but when Mary mails he first letter to him she already knows it's "Max."
Plot hole: When Norm is stuck under the satellite tower after disposing of the condos, he has flashbacks to numerous moments earlier on in the movie. One of the flashbacks is of Socrates saluting Norm, but the moment where Socrates salutes Norm did not occur until he was on the cargo ship being shipped off to New York and was something that he did not see Socrates do; there would be no way for Norm to have this flashback. (01:18:00)
Plot hole: Rafe is not a supernatural being, and besides not suffering any fatigue at all missing his sleep to do his pranks, some are outright impossible to execute and perform overnight for a person of his age (most likely for an adult in their prime too). Covering the entire hall and corridors, plus the principal's office, with post-it stickers requires a ridiculous amount of stickers to begin with, and arranging them creatively covering the whole walls, floor to ceiling, so that they create drawings, is an insane concept. Even more insane when it's the opening prank, anything he does later in the movie including the big movie finale requires less labor and time than his first act did.
Plot hole: Cruise leaves Lugnut to go buy he and Coupe some seats and mere seconds after leaving, Coupe appears in the scene and talks with Lugnut. Coupe asks if he has seen Cruise, but even if Cruise had already left to go buy tickets, Coupe would have already seen him when approaching Lugnut since she only arrived seconds after he left. (00:09:15)
Plot hole: When The Ray is injured on Earth X and has Red Tornado's cortex, he escapes by Vibe sending him into a portal to safety. However it is evident that Vibe doesn't know where he sent The Ray or where he would be going as later he's trying hard, searching the multiverse for him. Yet somehow The Ray is able to go across universes and winds up coming out right at Earth 1's Ray's feet to transfer his powers over to Ray and give him the Cortex. This makes no sense. The Ray can't control Vibe's powers or where he sends him, so he would have had no way of making himself exit the portal in Ray's back yard. And if Vibe sent him there on purpose, he wouldn't have been struggling to figure out where he went. The only way it makes sense at all is for it to be the most massive co-incidence possibly imaginable where he accidentally was sent to another universe and happen to come out right at the feet of that universe' version of himself. None of it adds up. (00:09:50 - 00:16:50)
Plot hole: Luka sneaks into Bayonetta's hotel room and plants a hidden microphone. While sneaking out, he is caught. That's when he is astonished to find a child with Bayonetta who calls her "mummy." He does eventually escape the room and sits in corner with his radio, surprised that they both went to bed and he receives nothing. The problem is: One must be an idiot to plant a mic in a lone woman's hotel room in the dead of the night, unless he truly enjoys listening to her snoring! Planting the mic in her apartment or office, or on her mobile phone makes a lot more sense.
Plot hole: Alberto didn't sign up for the Portorosso Cup, and he enters anyway. This should've gotten Luca disqualified.
Plot hole: Kaiba explains that his Blue-Eyes Shining Dragon gains 300 attack points for every Dragon-type monster in his graveyard. The monsters shown in the graveyard are three Blue-Eyes White Dragons, Blue-Eyes Ultimate Dragon, and Rare Metal Dragon, totalling 5 Dragon-type monsters, meaning Shining Dragon gains 1500 extra points. However, he also summoned Paladin of White Dragon earlier (which is a Dragon-type monster) and was destroyed, but is not included among the Dragon-type monsters in his graveyard. (00:54:15)