The problems with "tracking him down" are the lack of information, and the lack of time. Everyone knew Zoraal Ja had a dangerous ambition, but he never gave any inclination that he was going to take a run at his old man. The obvious time for him to act on that was during Wuk Lamat's coronation and he wasn't even in the city; and as far as I remember, nobody knew about the stolen keystones until his attack. To all outside the time bubble, his attack was so far out of the realm of possibility that it was never a consideration of finding him and taking him into custody. No one is at fault for acting, or failing to act, on information that does not exist.
As for the lack of time, as I understand it only a few days had passed between the coronation, the appearance of the time bubble, and the attack on Tuliyollal. When unlocking elite hunts, you meet a huntress that had been trapped in Solution Nine for thirty years, but the guy at the hunt board says, "I can count the hours since she left." It isn't unreasonable to assume Zoraal Ja is just... somewhere else. It hasn't been that long, so nobody would consider him missing, or that he might be planning something big. Again, how do you fault anybody for failing to act?
This is a good illustration of what I mean by "a lack of spatial and temporal awareness." We never have a good idea of how big the world is. There are implications of long travel times between places, but everyone just shows up exactly when they're needed (a problem this game has always had).
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Just as in Stormblood, when the introduction of Doma hurt the world-building of both it and Ala Mhigo, the introduction of Solution Nine stopped any development of Tural. Instead of facing yet another existential threat to the entire planet, we could have had our "low-stakes adventure" with a tighter, more local story, navigating the intricacies and intrigues of regional politics. We could have learned more about how the Dawnservant's goverment worked. Maybe the Landsguard is split into two factions, one that supports Zoraal Ja and one loyal to the throne. Maybe we stop Zoraal Ja's coup; or maybe we don't and he cracks down on foreign influence, making our character an outlaw. There are tons of possibilities here.