I thought the issue was that "broken windows" was used as a metaphor for all low-level infractions, and not literally interpreted as "fix the windows and clean up the graffiti" as the studies recommended. This then got implemented as quotas on police departments, leading to opportunistic, biased policing and the de facto criminalization of poverty.

As a result, the term "broken windows" now carries a ton of baggage, and is sometimes used as a racist dog whistle.