Maybe with flying that high someone got sick in that one so they had to send it on with no one until they could get someone to come clean it up. Hey it happens.
I haev seen weird things like that happen in the rides a lot. I have a ride room that consists of about 7 rooms and people fall off of them all the time.
Sometimes they end up backwards. Wow - they miss the entire attraction.
I saw the same thing on the first day that the SITS pin changed and I rode a few times! I was like, wait a second ... huh?! My automatic thought was that it was such a waste to send an empty car through the ride when people could have been on it (haha, as if we were really at WDW).