CTN4AS is an example of a Eurocontrol’s call sign similarity service that causes flights in Europe to use an alternate numbering.
FlightAware has logic to attempt to match up those flights so that they appear on our site with the airline’s true flight number, however this logic works best when each of the affected airlines provide their flight number mappings to us in advance. When they do not, our heuristics attempt to match it based on other criteria, otherwise it will appear on our site as a “position only” flight.
By default, “position only” flights are hidden from our site and APIs, specifically in the way that you have proposed to “discard these data”. Note that if you view that flight on our website it actually says “Tracking data for this position-only flight is incomplete and potentially inaccurate.”, which indicates that you have explicitly opted-in to viewing those types of flights. If you opt back out, you should see fewer of those types of flights.