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> In this case, the "a few bad apples are not representative of a group" meaning have grown above the "One bad apple spoils the barrel" meaning

Most of the time when I hear the "only a few bad apples, the rest of us are fine" meaning it's coming right from the mouths of badly spoiled apples twisting the meaning of those words and popularizing that usage to suit their agendas.

Generally, I think that there's nothing wrong with pushing back against words and phrases used incorrectly. We get to decide how words are used, and a large part of that decision making process involves social pressure and education. I think it's particularly useful to defend the meaning of words and phrases when they're being deceptively misused and promoted.