You are 100% correct ... the two aircraft are likely to be sharing the same air route, usually departing FROM the same airport and both going TO the same arrival airport. Often, they are scheduled to depart at the exact same time (or near enough to). Most times this will be two different airlines, meaning that their schedules just happen to match by pure coincidence.
This can also happen if there is an airport in the middle between two other airports, in a straight line, and a plane that's already in the air from the first airport is "intercepted" by a plane that has taken off from the middle airport and both just happen to be going to the same destination airport. It's just a quirky fate of the scheduling that causes this one.
Another possible cause of this is when you have TWO or more AI .bgl files loading. If both of these AI .bgls are due to your editing the AI schedules in the Traffic Controlcentre, and then innocently saving and compiling your work with different filenames ... then you will end up with the SAME SCHEDULES, compiled in to TWO (or more) .bgl files ... EACH of which will load in to the sim. This would therefore, create DUPLICATED AI aircraft.
The way to fix this is to use appropriate tools to locate details of one of the AI aircraft and then adjust its schedules (or, if you choose, delete it). The FSX SDK Traffic Explorer provides a great list of all the AI aircraft both on the ground, and flying, and can give you details about the airline, flight number, scheduled times, and departure and arrival airports. This makes it very easy to find the aircraft in the Traffic X or Traffic 360 schedules and do your edits (or deletions) accordingly. Remember, any time you edit/adjust schedules, or do deletions, you must recompile the AI .bgl file (whilst noting paragraph 3 above, of course). Or, if your issue is occurring because you happen to have two (or more) AI .bgl files containing the same schedules, simply remove one (or more) of them out of the folder. That said, if you do feel you need to make and save more than one AI .bgl file to suit your style of editing requirements, then you just need to take extreme care to ensure that each of your files does not contain the same flight schedules as any of the others.
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