The empty car should not have been left out on the track. It seems that someone sent out empty cars to 'test' the ride was ok after some 'maintenance problem' which had shut the ride down for an hour or so.
If x cars went out on the track to test it, then x cars should have been counted back in before reopening the ride. The crashed car was the first out after this and, because there was an empty car still stranded on the track a crash resulted, allegedly.
Human error here I suspect. I wonder exactly who was manning this ride? My experience is that they are too often manned by young people, on minimum wages. I worked for Merlin Entertainment for a season after I retired, just for fun. Many staff were seasonal, students. I noticed that Alton Towers is still closed today to 'add another layer of safety' said a spokesman, while 'staff training' was also mentioned. Other rides are also closed at other Merlin owned attractions for, presumably more staff training.