It’s time to remind ourselves what the “rotten apples” metaphor means and what it does not. It means that a even very few corrupt individuals in an organization need to be detected and dealt with quickly, because the rot otherwise quickly spreads and infects the whole system. Someone getting away with stuff is an object lesson to his peers.
It does not mean that a problem is limited, minor, and atypical of the system generally. It is incorrect usage to say of a scandal that it is “just a few rotten apples, not the whole barrel” and it is also an ethical and managerial blunder.