When Scrat's finished fighting the piranhas, he gets his acorn out of the one on the bottom of the screen. Yet the one that actually swallowed the acorn was smacked off-screen to the right.
At the beginning of the movie, Sid is standing at the top of the huge ice wall ready to jump down the waterfall. Sid starts counting "1,2.." and by the time he counts "2 and 4/1000" Manny and Diego reach near him. A few minutes later when the camera zooms out (showing that all the ice is melting), we see that there was no way any of the 3 animals could have climbed such a high mountain at all.
When Sid is tossed from the branches to the ground back at his camp, one of the young animals that watches him fall, a Macrauchenia (the trunked, long-necked animal), is gone in one shot, and then instantaneously appears on the other side of the screen.
In the end, Sid and Diego see the tribal mini-sloths and speak to them. In the next scene when the herd of new mammoths enter the valley, the mini-sloths have completely disappeared.
When Sid first starts singing the Food song, Crash and Eddie are sitting on Ellie's tusks. In the next shot, they emerge from behind her ears.
Opossums have a lifespan of 2-4 years. In the scene where Ellie meets the opossum parent and two clinging offspring assumed to be Crash and Eddie, she is an infant. If our related mammals the elephants are any clue, Ellie could not have possibly reached adult maturity before age 18. Her opossum brothers should have been long gone.
A young aardvark is seen blowing bubbles in a pool of melt-water, by breathing out through its elongated snout and in through the mouth at its base. Real aardvarks have tiny mouths, and they're located at the tips of their snouts, not underneath them. Keeping the end of its snout continuously submerged should've drowned it.
During the Herd's migration from the ice dam, Sid sings songs about mammoth extinction to the tune of Frank Sinatra's "The Way You Look Tonight", Buffalo Springfield's "For What It's Worth" and the children's song "If You're Happy and You Know It". Though these songs that would not come to exist for thousands of years, coincidences are always possible.
When Scrat sniffs for his acorn, submerged under the ice, his saber teeth are clearly not modeled before he sinks them into the ice.
When Crash jumps onto Diego's shoulders, as he is reaching the ground, slow motion of the film reveals that part of his face disappears.
When Manny looks into the pond at his reflection right before meeting Ellie, a leaf lands in the water creating a ripple. Manny's reflection does not distort when the ripple goes through it.
Given the implied size of the bowl, water would not have drained out of the crack so quickly at the end.
What are clearly oak leaves floating on the surface of the water have just fallen from an exclusively coniferous forest.
The two sea reptiles (Cretaceous and Maelstrom) were frozen in the ice, but in the era that they lived in, there was no place on Earth cold enough to generate ice.
As with the first film, many of the animals shown did not live either in the same period or place.
For much of the movie, Diego shows a great fear of being in water. In the previous film, Ice Age (2002), Diego shows no fear or hesitancy to enter the river while chasing the baby and his mother.
Sid is wrong. Tigers, and all cats, do have the ability to swim, and at an early age, too.
Condors don't eat acorns (but nobody ever told that to this condor).
When Fast Tony is talking to the animal about how he can help her lose a thousand pounds she clearly has ears that even flop around when she moves her head but when her mate walks into the shot to tell her she is "already as thin as a twig" her ears are completely gone.