I was once on it here in Hollywood and we all had to wait in the second car after we boarded because the front one had rolled into the station with vomit all over it. Someone puked all in the front row, and the team had to do their best to clean it all up. Then they ran the train empty to air it out. I've seen the same thing happen at Magic Mountain (though I'd imagine with Coronavirus fears right now, they wouldn't really want to risk it)
It could also be something like a sensor issue, which would probably be the issue in your case since you said they stopped everyone and ran it then and there. They'll run an empty train if something is funky to make sure everything is okay (and for guest safety, obviously.) Or it could be something else entirely!