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?
Suggested correction: They weren't sure about the baby dinosaurs' species because dinosaurs were thought to be extinct. The mother dinosaur eventually showing up, with her more convincing dinosaur properties of being much larger and menacing-looking, convinces them otherwise.
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.
Suggested correction: He is standing on his feet all this time, I recommend watching the movie.
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.
Suggested correction: He landed on the ground where he could possibly grab a leaf. How he got it up the tree is still inexplicable.
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.
Suggested correction: Inside the eggs they were bent and arranged much more compactly, the size is totally correct.
Stupidity: Rescuing Manfred and Diego from the giant carnivorous plant, Buck could have cut both wires simultaneously to avoid that unnecessary horrible potential outcome of cutting the wrong one. The wires were stretchable enough for them to have been held together to then get cut at the same time. (00:37:40)
Suggested correction: Cutting both wires simultaneously would probably cause a different effect. Besides, Buck isn't very intelligent.