[caution: good-natured linguistic pedantry follows. Apologies in advance!]
As a point of interest, this usage of "bad apple" derives from the old folk wisdom: "one bad apple spoils the bunch".
Unlike quite a lot of old folk wisdom, this saying is literally true: mold growing on one apple will quickly jump to and colonise other nearby apples, and overripe apples emit a gas which causes other nearby fruit to ripen (and then overripen) much faster than normal; so it's important not to store overripe/moldy apples together with regular fruit!
Anyhow, my point is just this: "bad apples" doesn't mean that something is in the minority and therefore doesn't have much effect and can be safely ignored -- it means that something is in the minority but is likely to infect everything around it if urgent action isn't taken to separate them. If that wasn't your intended meaning, then "bad apples" was definitely the wrong metaphor to reach for. :)