When Manny, Diego, and Sid are on the ice floe with the giant crab during the storm; as the large wave approaches, Sid grabs the right fore leg of the crab. As the go through the wave, Sid is still holding the right fore leg. When they emerge from the wave, Sid is now holding what would be the left fore leg (it curves left (when facing the crab) back into the body).
Many of the pirates' weapons switch places and hands during the land bridge trap sequence.
Firstly, Gupta, on Gutt's order, gives his dagger to Louis, who leaves it behind when he digs under the ice. When Gupta and Flynn chase Sid and Granny to the ship's underbelly shortly after, he has Gutt's dagger instead, which Gutt dropped at the ship's front when Louis smashed ice on his foot, and Flynn, who previously possessed a skull sword, has Raz's spear, which vanished from her grasp inexplicably after Manny broke free. Then, as Gupta and Flynn flee the ship's underbelly, then leave their weapons behind.
As we cut back to the ship's topside, Raz has her spear back. Gutt is initially weaponless, but has his dagger back at the pirates corner Manny, Diego, Shira, Crash and Eddie. Gutt also has his original dagger back, and Flynn has his skull sword back. Then, in the shot where Precious blasts Gupta, Razz and Flynn, Gupta, Flynn and Gutt are all unarmed, while Raz's spear in knocked overboard with her.
When Peaches cuts Ellie free shortly after, she does so with Gupta's dagger, tossing it away from the ship's front after. Finally, when the floe Manny and Gutt are on is raised by the seabed rock, the floe is initially weaponless, but gains Raz's spear, Gupta's dagger, Flynn's skull sword, and another sword knocked from Raz's punch earlier, all of which were in different locations. All four weapons are either lost overboard or broken during Manny and Gutt's fight.
During the chase at switchback cove, Manny 'holds Sid higher,' and promptly hits him against three trees. In the next shot, they are on a ledge, and no trees are in sight. In earlier overhead shots of the area, there are also no trees seen along the path used.
During the sea shanty "Master of the Seas", Shira is at one point to Gupta's left, but in the shot in which he plays the fife, she is to his immediate right.
During the chase at Switchback Cove, when Manny, and Diego leap onto the ice floe, and Manny catches Sid, Diego (with Granny on his back) is on Manny's left. But in all subsequent shots, Diego and Granny are on Manny's other side, until Diego slams into a ice rock leading up to the ice ship.
Granny is seen feeding fruit to her "pet", Precious the whale. Whales are all carnivorous.
After Manny pulls down the mast the "pirate ship" breaks in half and sinks. This is impossible because the "ship" is an iceberg and ice floats.
Precious, the whale, is depicted with both a blowhole and a pair of nostrils just forward of the eyes. This is impossible - whales' blowholes are their nostrils.
Apes and monkeys have short, blunt fingernails similar to those of humans. They would be completely incapable of gutting someone, as Captain Gutt claims.
Louis is referred to as a rodent by one of the young mammoths, yet he is supposedly a 'mole-hog'. Neither moles nor hedgehogs are rodents.
When Peaches stormed away from the other teen mammoths, she was supposed to disappear from the shot but her back fur can be still seen in the bottom left of the shot, indicating that Peaches' character animation froze there.
As in most installments in this series, many of the animals depicted did not live in the same time or place.
Several of the animals aboard Gutt's ship are carnivorous - Shira and the elephant seal, for example - yet all the "pirate booty" is fruit and vegetables. What are these characters eating?