In Universe, the JP3 Raptors are a separate version to the one in the first and second films. The JP3 Raptors were the first version of bred by INGEN. But they proved to be far too intelligent to be handled and especially too dangerous for a park setting and so revisions began to try and create an animal that was easier to manage. This is why they look different too. More of something else in their genome to try and offset the hyper intelligence of the JP3 Raptors and BAM, you get the more savage (though still intelligent, just not AS intelligent) version we see in JP and TLW. However they were STILL too much and so research began on Nublar to breed an even safer Raptor that could be hand-raised. This is what Wu was doing in Jurassic Park with the eggs and hatchling Grant held AND what he successfully did in Jurassic World with Blue, Delta, Charlie and Echo. The first version however (JP3), were released, or escaped during or prior the Hurricane that destroyed the INGEN facilities on Sorna and they took up territory on the West side of the island (TLW took place on the East side). The striped animals you see in TLW are the males of the adult Raptors from the first film. Hammond was too soft to destroy his failed attempts. So there it is. You have the original Raptors bred on Sorna (JP3), which were superseded by a modified version designed to be safer but which still proved far too dangerous (JP and TLW) and then you have the latest versions which were even further modified and hand-raised this time (JP HATCHLING and JW RAPTOR SQUAD).