In Jurassic World, before releasing the raptors in for tracking the Indominus Rex, Owen lets them smell the flesh of Indominus Rex, which also had a tracking implant. However, in the movie, this implant was found by ACU when they went to capture Indominus. But all those members got killed and Owen didn't go there. So, how and when did he get that implant?
According to the film's "Special Edition: Junior Novelisation", several of Hamada's troopers did in fact escape from the I-Rex™ and returned to base shortly afterwards. It's notable that they had sufficient time to collect their fallen colleagues (and their kit, and presumably the tracker) before they left the scene, especially given that once they started firing live ammo it was the dinosaur that made a sharp retreat, not them:
The Indominus hurled Hamada to the ground, stomped on him, and swiped another trooper with her tail. The troopers fired nets at her, but she easily tore them off and chomped another trooper.
The remaining troopers picked up their fallen comrades and stumbled back toward the vehicle. One of them pulled out a real weapon and fired live ammo at the Indominus. The bullets pinged off the bony plates on her back as she turned and raced into the jungle.
The order of the scenes is important.
- Indominus is chipped.
- Indominus gets loose.
- The retrieval squad follows the tracker.
- The retrieval squad finds the tracker was removed by Indominus.
- The retrieval squad take an unexpected tour of Indominus' digestive track.
- At some point, Owen or another retrieve the tracker + Indominus flesh.
- Owen uses the tracker to give the raptors a scent to follow.
Getting the tracker later on would be a minor plot point that would be unnecessary to show. It's a tracker, and still works. They know exactly where it is. All that is needed is for someone to drive up and get it.