If it is silverlight, it's possible that "cognitive anomaly" refers to the anomalous region of the cognitive realm that the city is located in. It's been heavily implied that silverlight doesn't have a physical realm analog (likely if you transitioned there, you would end up in space), which begs the question of how there's enough space in the cognitive to build a city there. Perhaps the anomaly is an expanded region of the cognitive realm where one would expect nothing (since no one is thinking much about that particular patch of space), and the anomalous property is that it exists at all, not that there happens to be a city there.
As for why Nazh didn't mark that silverlight was in the anomaly, we've seen exactly zero cities/non-natural structures marked on these charts so far. Perhaps it wasn't worth mentioning when it would be obvious to the users of the chart.