[dataflow]

I don't think the phrase has changed meaning?

> The phrase originally meant that one bad thing corrupts and destroys all associated.

It's saying if you don't remove the bad apple, you will get a lot of bad apples in the future. The presence of a bad apple doesn't imply all of them are already spoiled right now. If you're seeing other apples that still haven't spoiled, it suggests you still have time to do damage control. That seems consistent with how the metaphor is used nowadays.