I kind of think this is also a bit misleading. Isn't the point of the phrase that you should remove the bad apple lest it affect the rest. As in, "If you leave the bad apple in the barrel it will spoil the bunch. So remove it before it does." I don't quite think that its really being misappropriated.
From your link a translated original proverb:
“Well better is a rotten apple out of the store
Than that it rot all the remnant."
So, by that logic, if you get those bad apples put before they spoil the bunch then they were "just bad apples".
To be clear I'm not saying the phrase isn't being used to minimize serious issues. But the point of the phrase wasn't that one bad apple means the entire bunch is already rotten, but that you need to remove the bad elements before the rot spreads.
Quite a range of things. It's so many It's hard to list them all. Some of these are more global than others:
Eyestalk ablation is the removal of one (unilateral) or both (bilateral) eyestalks from a crustacean. It is routinely practiced on female shrimps (or female prawns) in almost every marine shrimp maturation or reproduction facility in the world, both research and commercial.
Chick culling or unwanted chick killing is the process of separating and killing unwanted (male and unhealthy female) chicks for which the intensive animal farming industry has no use. It occurs in all industrialised egg production, whether free range, organic, or battery cage.
A gestation crate, also known as a sow stall, is a metal enclosure in which a farmed sow used for breeding may be kept during pregnancy.[1][2][3] A standard crate measures 6.6 ft x 2.0 ft (2 m x 60 cm).[4][5]
[...]
There were 5.36 million breeding sows in the United States as of 2016, out of a total of 50.1 million pigs.[8] Most pregnant sows in the US are kept in gestation crates.
Ventilation shutdown (VSD) is a means to kill livestock by suffocation and heat stroke in which airways to the building in which the livestock are kept are cut off. It is used for mass killing — usually to prevent the spread of diseases such as avian influenza. Animal rights organizations have called the practice unethical.
The one that got me most was Thumping, the standard operating procedure for killing baby piglets. They grab them by the back of the head and smash them into concrete until they're dead, depicted ~6 minutes into Dominion