Common app will release their first report of this season’s app volume in the next week or two, here: https://www.commonapp.org/about/reports-and-insights
Of course common app doesn’t have all the app volume (probably 60%-70% or so)…the UCs have significant volume, and many schools also offer their own app.
I assume you are talking about college specific pages in Naviance? Naviance is generally set up to only pull colleges applied to, but counseling staff can enter some data manually if they choose. The school counseling staff would be the ones to tell you what the Naviance data show, they are in control of what is in there.