I know between the masses of new Metas, the Schools/Institutions retrofitted to house and keep them more or less segregated from the general public as a cure is mass produced and to ensure they don't wreck havoc on the people as they likely can't control their powers. 

And the loss of public trust as people will begin to wonder what the heroes have been doing as they'll argue even dispute evidence to the contrary the heroes should have saw this coming or something. Like they're some omnipotent things.

There's going to be people, senators, lawmakers, and anyone involved in politics trying to spin this situation into something favorable to them and their agendas. Like Sampson. If he has his way Heroes would have to go through proper channels before arrests can be made or villains can just walk due to evidence tampering and whatnot. Anything to make a Hero's life difficult.