Generally duplicate flights are the result of 2 or more add-on ai traffic files scheduling the same flight.
An example of this might be if you have installed 2 seasonal traffic files for the same airline.
A good tool for identifying the source of duplicate flight plans is the FS SDK Traffic Toolbox>Explorer, which if installed and activated is available in the 'Tools' menu in the sim. With it you can identify the files that contain the duplicates.
If you use FSX (Deluxe or Accel.) it is installed with the SDK . You may have to activate it in the DLL.xml file.
If you use FS2004 you can download the Traffic Toolbox SDK here-http://www.fsdeveloper.com/forum/downloads.php?do=cat&id=10
At that time  the chief engineer was almost always the chief test pilot as well. That had the fortunate result of eliminating poor engineering early in aviation.