Because AoS can never, ever do anything right by some folks.

Is it not fairly clear that realSHIELD's aims are to eliminate or violently subdue supers? That that's the real reason they went after Coulson's team… not because Coulson is a bad leader, not because realSHIELD cares so much about Fury's secrets, but because Coulson has better means to identify supers (the Toolbox)…