(at around 42 mins) When Kowalski says "Nope, I still can't read", it's a reference to the first Madagascar (2005) where he says "Sorry Skipper, I can't read" when the sign says the ship is going to Africa.
Dave's direct orders to his octopus cronies incorporate a famous actor's name, e.g. "Drew! Barry! More power!"; "Anthony and Michael, haul them away", "Nicolas, cage them!"; "Charlize, they're on the ray!"; "Hugh, Jack, man the battle stations."; "Halle, bury them."; "Kevin, bake on; we're still gonna need that victory cake."; "Robin, write this down."; "Helen, hunt them down!"; "William, hurt them." ; "Parker! Posey! Go all terrain!" ; "Elijah, would you please take them away?". The relevant actors are Drew Barrymore, Anthony Michael Hall, Nicolas Cage, Charlize Theron, Hugh Jackman, Halle Berry, Kevin Bacon, Robin Wright, Helen Hunt, William Hurt, Parker Posey and Elijah Wood. The idea had already been used two years earlier in A Fuga do Planeta Terra (2012).
(at around 26 mins) The sheep that North Wind was holding hostage is from the Dragões: Pilotos de Berk (2012) series also produced by DreamWorks Animation.
(at around 5 mins) Skipper's order, "Don't shoot until you see the whites of their eyes," is an 18th-century military command most famously given by William Prescott at the Battle of Bunker Hill, Massachusetts, in 1775, against advancing British soldiers.
Originally scheduled for release in March 2015, the film was completed ahead of schedule, allowing the release date to be pushed up to November 2014, swapping release dates with Cada Um na Sua Casa (2015).