Why broken plot? The WG has managed to stay in power for 800 years by operating how they operate.
Do you expect them to send a buster call every time someone with the Gomu gomu no mi appears, just so the fruit can respawn? He wasn’t a serious threat and no signs of awakening. They also said why is the fruit awakening now? They were unlucky that he was out of their grasp when the fruit awakened. And they have tried to kill him but not managed. Akainu and kizaru went after him on Marine Ford. But it wasn’t meant to be.