When the asteroid cracks in half the acorn is on the back of it but when we see it heading for Earth it's on the side of the asteroid.
In the beginning of the movie when Scrat's acorn splits the asteroid heading to earth in half, the acorn is travelling with the asteroid. However the next scene Scrat appears in, he has his acorn with him in his spacesuit as he crawls through a support line back to the spaceship.
Shangri is referred to as a llama, but has horns, which llamas don't have.
The Dino Birds' wings are way too small to be able to allow them to fly but they're able to fly anyway.
When Scrat is banging around the planets shortly after first leaving Earth, causing them to bounce around like balls in a game of pole, Saturn is shown to have bounced through space, off the rings, and to role into the center. This is not possible considering that the rings would first have to have a center of gravity to orbit around before they could form, and the rings are made out of small chunks of ice, would not likely be able to take the collision of a planet of that size, causing them to be scattered upon impact.
Most of the animals in the film didn't live in the same time or location.
When Scrat is in the asteroid belt the asteroids are close to each other though they are very far apart.