In certain shots, when the Ornithocheirus flaps its huge wings, a segment of its wing membrane seems to become detached from its arm, as you can tell by the thin dark line that appears between the arm and the membrane.
The shot of the Iguanodont youngsters playing with the Polacanthus has been either flipped, or the Polacanthus decided to walk in the opposite direction for a moment. In either case, it's heading in the other direction again a couple of seconds later.
Ornithocheirus is not the largest pterosaur ever to have lived, as the program claims - that title belongs to either Quetzalcoatlus (which appears in the documentary and is described being bigger) or Hatzegopteryx. It is unlikely that Ornithocheirus' wingspan could reach 12 meters. The largest known specimen only has a wingspan of 6-9 m. The specimen on which the show's size estimates had been based weren't properly described until more than a decade later.
According to the narrator, the pterosaurs' wings were made of thin, easily damageable skin. In reality, their wing membranes were a complex organ with muscles and stiffening rods supporting them, and were much more durable than simple skin.
When we first see the herd of Iguanodonts walking along the coast line, one of them wanders off to the left side of the screen. It seems to be missing its right hind foot! Its leg just ends without a foot as it walks. It can be assumed that this specimen has simply been injured, however it doesn't limp, and there is no indication as to what could have bitten off its foot. Thus, it is most likely an animation error.
In one scene, an Iguanodon starts running and leaves distinct footprints in the sand. However, when it is about to start running, there are no foot prints behind it at all, as if it had been standing there for days.
As the two Utahraptors are trying to bring down the Iguanodon, the foot of the left raptor switches from being on the Iguanodon's hind leg to its front leg in a matter of frames. At the end of this whole sequence, as the Iguanodon is finally brought to the ground, you can see that one of the Utahraptors is biting its neck. If you are quick, you can spot some of its clawed fingers disappearing into the neck of the Iguanodon and passing completely through it to where they belong: on the other side of the neck.
When the Ornithocheirus starts calling out to attract females, its head is clearly a puppet, as on the bottom corner of the screen you can see part of the puppeteer's arm, head and even wires hanging out of the puppet's neck.
Near the end of the first shot showing the Ornithocheirus mating ground, the two animals next to each other on the left are making the exact same motions. Of course, nearly all of the animals were animated to repeat only one set of motions, but these two are making them at the same time.
As the male Ornihtocheirus soars above the crowded mating ground, in one badly rendered shot, he flies behind the crowd, and the animals resting on the ground suddenly appear to be exceptionally tiny. Yet he himself remains to be gigantic, even though he has already flown into the background. The animation layers must have been mixed up.
The water that burst out of the blow-hole clearly passes right through the Tapejara that's sitting atop the cliff. Although its movement indicated it's shaking water off its body, the animators forgot to make it look wet, and the splash effect is also missing.
As the Ornithocheirus catches a fish, you can only see the head of the animal, even though its body and its huge wings are also supposed to be in sight. They must have forgotten to animate the rest of its body into the shot.
When the narrator talks about the mutual protection between Iguanodon and Polacanthus, a large Iguanodon walks by, but there is a thin line on the bottom of the screen where the background is visible through the Iguanodon.
There are blurry outlines around the three small pterosaurs that fly over the sea. This is because the original shot featured three birds, and the CGI crew failed to erase them out of the footage properly.