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It sounds like you may have switched the aircraft out of programmed flight mode to land. We recommend keeping the aircraft in programmed flight mode at all times and just using the sticks to adjust the landing. If you must switch out of programmed flight mode you need to make sure it is back in the programmed flight mode before landing and the warning recommends. Otherwise the waypoint sync will be off.
If this was not the case and the aircraft deviated from the blue path verification that was acknowledged at takeoff then you may have a hardware issue. This sounds like a waypoints sync issue though.
If you continue to have issues please send us the flight log from the affected flights.