I bet it's not just New York. Similar incentives are in place all over the country.
I found it interesting in the article that the judge says "He said that while the vast majority of cops don't engage in crooked practices, it was common enough to be an institutional problem." Paraphrased: this is not really a problem, this is a problem.
And exactly how would he even know that "the vast majority of cops don't engage in crooked practices"? Just one of these happening is bad enough, imagine sitting in jail for a crime you didn't commit and then multiply that over it being common enough to be an institutional problem.
And lastly, I didn't read anything about the officers going to jail for possessing large quantities of drugs. If these two innocent victims weren't the ones that either had drugs or interacted with the officers, where did the drugs come from? The officers.