When the Founder is making the deal with Stephen, the flash drive in his hand changes orientation repeatedly from shot to shot.
They know the name of the breakout, Cassandra Smythe. They know she is the daughter of the Founder. Yet they can't deduce the name of the Founder.
In the pilot Stephens father said he had hoped Stephen had taken after his mom and been human but later we find out that she has powers like Stephen and his dad, and that Roger was aware of them.