Hi Hector,
Sorry for this sad story... of which I can answer to some parts.
The most disturbing of it being the wrong flight selected. The reason is that in FL3, when you press the "ProPilot" button, WHATEVER flight, airport or aircraft you had previously selected are overriden with the flight, airports and aircraft of your booked flight.
I admit this is not very intuitive, especially that you are prompted to confirm "this flight", although this does not mean the flight you see on screen. This bit will look differently in FL4, but this is "almost implemented" for the moment.
The other big problem you mention is already solved in FL4. There is now a check whether the flight - as performed in FS - starts and ends at the good airports for the flight one has selected. This was one thing I tried to solve since my earliest days in the project...
However your misadventure gives me a further idea: should the FL warn IN FLIGHT when the pilot is heading in an obviously wrong direction? A subject of debate, especially the part where "obvious" is to define.
At this time, the only warning a pilot can have comes from the ACARS page within the site, which would have clearly shown the misunderstanding. I use it sometimes, but not always.
What more can I say? Sorry for the IVAO flight and definitely sorry for the furious girlfriend. Virtually furious, I dare hope...
Now about deleting the flights, this may be necessary at IVAO if someone picky sticks his nose in our PIREPS (but I leave this to Murray to decide, I think he knows better). However I would not delete the flight from our database, I have seen times and fuel burnt way stranger than yours.
Andrei