Because the 3rd movie is on a different part of the island from the second.
From the script of The Lost world: (showing that some of the dinosaurs gathered in different parts of the island)
LUDLOW (cont'd) Our infrareds show their nesting sites are concentrated in the island interior. That's why we planned on
keeping to the outer rim.
Offering weak support for this as well is this excerpt from JP3 wiki:
The landscape of Isla Sorna is very drastically different from that in
The Lost World. [snip]..., although this could be because the parts of the
island seen here are in the lowlands of the island which is tropical,
while the sections scene in TLW is only from the highlands of the
The other part is also explained in the script for JP3. There were things that InGen was doing that were not disclosed to the public.
GRANT Not with that sail. (Billy gives up) Spinosaurus
BILLY I don't remember that on InGen's list.
GRANT That's because it wasn't on their list. Who knows what else they were up to?
Out of Universe is the real answer
JP3 was not based on a book by Michael Crichton, unlike the first 2, and while it had some material from his novels it obviously was going to be different coming from script writers and not a novelist.
As for the appearance of dinosaurs changing, this is actually due to scientific finds during the period between films. Our view of Deinonychus* changed out of universe and they decided to be more scientifically accurate instead of keeping the look for continuity.
*The basis for JP raptors.