Why was messaging sent on a flight that is no longer booked?

This is often because when the itinerary had been updated to remove/change a flight or cancelling the PNR was never received by FlightStats. 

The "Itinerary Rule Histories" displays the history of when a PNR was received, updated, or messaging has been sent. To navigate to this page you will want to click on the "View Monitoring Rule" link found on the 'View Itinerary' page under "Related Links"

If updated itineraries are not being sent to FlightStats, you will want to check with whomever handles your mid-office/QC for your company about why updated PNRs are not being automatically loaded for FlightStats retrieval.