I think the larger "issue" is that the phrase colloquially means the exact opposite of the original observation, that a bad apple MEANS the bunch is spoiled. It's worse because this changing of the meaning is perpetuated by those same bad apples themselves.

"the proof is in the pudding" is a much more benign change. It's literally just a shortening, but no meaning is lost... if you want the proof, you'll find it in the pudding (implying you should try the pudding to verify your assumptions)