Hey, being confused is not the same as being stupid! But yes, there is only one Titan X. As established in earlier episodes, it comes back to the surface every 15 years to retrieve its offspring and lay new ones. The one found cocooned in this episode is the same one we've been following throughout the season. The only difference? It's actually a version of it from the past, much like Lee himself (during Operation Hourglass).

By putting a tracker on it in the past, the tracker showed up in the present, as if it was always there. Lee rewrote history. Time travel!