Plot hole: After the dinosaur kids wrecked the playground, Manny tells Sid, "Whatever they are, take them back" and someone says "What are they?" as well. Later, when Mummy Dinosaur appears, Ellie says, "I thought those guys were extinct!" and one minute later Manny says, "She's a dinosaur!" How could they possibly not see that the kids were dinosaurs if they already knew about dinosaurs in the first place?
Continuity mistake: In the scene where Buck tells about his encounter with Rudi, you see Buck swing back and forth on the gross pink thing. The next scene in the cave he is still swinging, "back and forth" but he's not hanging from anything.
Continuity mistake: When Buck recites his tale of how he lost the eye, he covers his eye with on hand (paw) and run up a bare tree. There are no leaves in the vicinity, and there is nothing in either hand (paw). But reaching the top, he ties the eye-patch.
Plot hole: The baby dinosaurs are small enough that Sid can carry them when they are still eggs, yet as soon as they are born they are twice the size they were inside the eggs. Their size shouldn't have changed that much, and even if it did the eggs would have been much too large for Sid to carry.
Plot hole: In the end of the movie, when Scrat is back on the ice world with the acorn, he mocks Scratte about it. However, the ceiling to the dinosaur world is thousands of feet up, so how could Scrat see and hear Scratte, and vice versa?
Plot hole: In the very end of the movie, when Scrat rides the rocket back to the ice world, it smashes a hole through the ice layer. Two mistakes follow: First, bits and pieces of ice fall away from the rocket. One can conclude that the hole is slightly bigger than the ice slab above, yet they fit perfectly together when the ice falls back down. Second, how can the ice separate from the rocket and fall exactly where it was before?
Continuity mistake: From a significantly far distance, Sid is seen rolling one of the dinosaur eggs to the other two and is originally seen on his way to push the egg to left side of the other two, but is instead seen pushing the egg between the other two in the following shot. Also, in the initially mentioned shot, there is no downhill slope to the left of Sid and the eggs. But magically, one appears right next to them two shots later. (00:12:15)