No contradiction. You can have one system, one small part of that system being no broken windows, where windows are commonly broken. You can have another system with unbroken windows. Repairing the windows and punishing people for breaking them won't magically transform the first system into the second. In fact, it might actually make things worse, depending on how it is implemented. For example, if it's already common to break windows in an area for a wide range of reasons and you start fining broke people money they can't pay and throwing them in jail... you haven't saved the windows, just caused a lot of damage.