Having played the role of leadership in different capacities across decades, Yahiko had a good handle on the little tells that exposed his subordinates.
If they constantly kept him informed, things were definitely going well.
If not, things were pretty bad—as was this situation.
But while not finding Claire was bad for Charlie, it was good from Yahiko's perspective.
Since Charlie couldn't find Claire, he would sooner or later lose faith in getting her back. And the first gradual step to that