sys·tem·ic : take it and run with it
Main Entry: sys·tem·ic
Pronunciation: sis-'te-mik
Function: adjective
: of, relating to, or common to a system
Of course it was systemic. The system of running the prison was faulty. The abusive acts could not have happened under a system that provided proper supervision.
The General's use of the word systemic in no way infers the system was faulty from top to bottom. You can perceive it that way if you choose but your perception does not make it a fact.