Timetable/Schedule glitch, Help!

I have lost around $50'000 already because of this glitch, please help!

When you last changed your timetable to you press activate in 3 days, or just activate?

I would not call it a glitch  ;)  you obviously changed your flight plan and then you usually have two choices .... activate immediately (which will be booked with 24 hrs delay) or you activate your new flightplan with 3 days delay. If you activate a flight plan it will be updated every 30 min., so at the hour and half past .... so the best thing is that once you modified your schedule you wait until it is booked in the system and then cancel MANUALLY the flights you don't want. With 3 days delay you mostly get the correct booking but maybe you need to book a transfer flight. The most trouble you normally have if you activate the schedule immediately since you have to manually cancel the flights ..... I normally activate my schedule with immediate effect, wait until they are booked and then cancel all the flights I don;t want anymore ....

I must have put it on 3 day delay, and then changed the schedule after those flights were set to take off, which duplicated it.

If you change the flight schedules for an aircraft, you need to check frequently (ie at least once a day) to see if AS has done this kind of double scheduling and cancel the flights manually.  I keep all recently changed flights in a fleet called "changed", makes it easier to keep track of them.