Stupidity: Why weren't any of the guards thinking of running to the base of the crane to stop it? Surely there was a more than fair chance to capture Frypan as he had to stay up there and swing the bus to outside of the wall and lower it. Not only does that take a long time, he had to climb back down again.
Stupidity: They could've used the flying chopper thingy to kill off the armed guys when rescuing the kids off the train carriages. That way they could have made sure they got every single kid rather than rushing to just take the one containing Minho (which they messed up).
Answer: Because Janson wishes to be the one in charge. He plans to cure himself and only the people he deems worthy, presumably so he can "rule the world."
BaconIsMyBFF