After Sid has seen the opaque babies through the shells at sunset, he walks up and puts his arms around all three eggs. As the camera pans back and moves to the right, the number of eggs changes from three to two. The egg in the middle vanishes and Sid is left with his arms around the two outside eggs.
When Diego first finds the tracks, Ellie makes several steps forward to join him. The next time we see her, she is standing next to Manfred again, with no indication that she moved.
When Buck agrees to help the herd find Sid, he drops his knife to his left. When he starts explaining the rules, the knife is missing from the background, but is visible again when they start to move ahead.
The 3 eggs are falling and Ellie manages to catch the third one. Then Sid walks down to where she is, carrying the other 2 eggs in his hands. But a minute later, (when Manny discourages him) he puts the eggs to the wooden sledge waiting nearby. The sledge was not there when Sid walked down. In fact it gets lost when Sid and the eggs are tossed into the air a few minutes ago.
An Ankylosaurus (large dinosaur with an armored back and tail club) is shown attacking the main characters when they first enter the dinosaur world. Though depicted as a carnivore, this species was herbivorous. Though some have speculated that it is merely attacking the group because it felt threatened, as a rhino might, it is shown with pointed, meat-eating teeth and is clearly supposed to be a carnivore.
Rudy retains a gap in his teeth where Buck knocked one out, and seems to hold a grudge against him because of it. In reality, reptiles have an endless supply of teeth - they fall out and are replaced throughout the animal's life.
(Around 50min) In Buck's flashback, when Buck fights Rudy, it is raining. This should be impossible since this scene takes place underground.
In the movie, a relict population of dinosaurs continued breeding for nearly 65,000,000 years after their kindred became extinct. They have been sequestered away, allowing them to evolve to larger sizes as the competition would be more fierce and would need to grow bigger for the need for resources. Also, 65,000,000 years is sufficient to evolve whole new taxonomic families and orders, as mammoths, sloths, cats and humans sprung from humble roots in a fraction of that time. Since the scope of this "what if" scenario can accommodate many speculations, alleged inaccuracies about size, color, posture, diet, etc., become redundant.
The dinosaurs famously died out millions of years before animals such as the woolly mammoth and saber-toothed tiger appeared. However it's stated in the movie that the dinosaurs they find are a few that managed to survive underground, and that the mammals thought they were extinct.
As in L'era glaciale (2002) and L'era glaciale 2 - Il disgelo (2006), some of the "Ice Age" creatures shown were in fact extinct before the Ice Age. (This does not count the "secret" dinosaurs they meet, which is not a goof as explained above, but to the above-ground community which Sid, Diego, and Manfred have always lived in.)
As in L'era glaciale (2002) and L'era glaciale 2 - Il disgelo (2006), the woolly mammoths' neighborhood includes creatures who in fact lived on different continents, and never saw mammoths.
While Crash, Eddie and Buck were on their way to save Sid, Buck says "roger" but Crash and Eddie couldn't understand the correct meaning. However, in L'era glaciale 2 - Il disgelo (2006) Crash and Eddie used the term "roger" with correct meaning while they were checking the perimeter for Ellie.
(Around 1hr 5min) Sid describes the lava as deadly and boiling. Although deadly, the lava is not boiling.