of the first problems that many people saw as a flub after Jurassic Park
3 came out was the confusion over the Pteranodons. Jurassic Park 3 purports
that the Pteranodons are locked up in the aviary and have not been allowed
to escape. Contradictory to this is the closing shot of The Lost World,
where it is clearly seen that a small flock of Pteranodons are flying free.
First, let's compare the flying reptiles as seen in TLW and JP3.
It becomes quite clear that these are two different species. Upon closer inspection, they are not only two different species, but the 2nd one-the one from Jurassic Park 3, are orange, brown, and yellow in coloration as opposed the blue and yellow coloration of their Lost World counterpart. Another difference between the two animals is that TLW's Pteranodons have 23 feet wingspans while the JP3 Pteranodons have larger, 32 feet wingspans. These all then become crucial clues in fact that the Pteranodons in Jurassic Park 3 are not true Pteranodons. 'Pteranodon' means 'winged and toothless,' which the ones seen in Jurassic Park 3 so obviously violate. The ones seen in TLW have no teeth and appear to be truer to form.
This entire subject put together seems to prove that The Lost World Pteranodons are free because they are actual Pteranodons, possibly docile rather than aggressive animals. The ones seen in JP3 are locked up quite simply because they are mutated monsters. They are far more aggressive - as seen in JP3.
Pteranodon had a high aspect ratio (wingspan
to chord length) similar to that of the albatross – 9:1 for Pteranodon,
compared to 8:1 for an albatross, therefore Pteranodons could fly long
distances like albatross.
The Pteranodons we see in TLW don't leave the island due to the fact they are probably very territorial and they have all they need to live there - fish, water, canyons, etc. They are free due to the accident at Site B, possibly because at the time of the accident they are only young and are in cages in the laboratory (seen in JP///) or they were always free due their, likely, gentle nature.
On the other hand the reason why the JP3 Pteranodons leave the island at the end is pointed out by Alan Grant that they are probably just looking for new nesting grounds as the world is now a new place for them.
(The theory of Pterandons flying long
distances has been put forward by Dr Dino)
there is no true flub here, only deeper fact that lies within.