The phrase that "bad apples" is taken from is "A few bad apples spoil the bunch". It's one of many phrases that has entered the common consciousness in partial form with the exact opposite meaning of its original intention.
His counterpoint is that a bad barrel can spoil a bunch of perfect apples. Good people can commit evil actions when they are put into bad social structures.
The spoilage in the "bad barrel" model comes from the containing structure, not from within its contents.
If you have a good barrel, you can keep bad apples more or less fresh. And if you have a bad barrel, even the best apples will spoil.
More literally: our focus should be on the command structures, accountability practices, disciplinary bodies, legal liability, and training programs within police departments -- rather than blaming systemic problems on a handful of white supremacists, careless brutes, or sociopaths.