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: There are two cars driving behind the EPA truck containing Marge, Bart, Lisa and Maggie. When Homer uses the bulldozer to try and break the family out of the truck, the two cars behind the truck don't notice the bulldozer trying to destroy the truck. There's no way they couldn't have not seen the bulldozer since they were just behind it. (01:00:05 - 01:00:40)
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: 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: I can somewhat understand that in a kiddies' show all aliens can inexplicably speak English - but using Terranean (i.e.: Arabian) numbers as well? While Tetrax's computer uses alien runes, the readout on Gluto's holographic HUDs use Arabic numbers - somewhat a bit too deliberate a producer choice to emphasize intergalactic communication.
