While Cersei was blowing up the Sept, Qyburn had his new "little birds" kill Grand Maester Pycelle.
Varys always used to refer to his "little birds," and on season six we saw as Qyburn finally met them and brought them under his wing. The birds are really just poor children who live in King's Landing.
On the season six finale, we watched as the little birds stabbed Maester Pycelle to death while Qyburn watched.