That is more of a question of the lack of a Centralization mechanic, which could justify and make interesting a lack of control over sectors in general or specific sectors in certain circumstances. A client state that has just been assimilated and turned into a sector, which still has different ethics and possibly a different governor, could just keep going on its own way, funding research rather than mining efforts or keeping a soft stance on slavery, unless the empire becomes centralized enough to strictly impose its policies on all sectors from above.
But that is an entirely different matter, the current setup is just bugged.