So this is purely anecdotal, but here's what I've noticed from personal experience
Any time I get into a private instance of Leap of Faith, I did the following: The instant the npc spawns, I'm immediately clicking on him. I click through the npc's dialogue as quickly as possible, and click on the entry option. When the queue pops, I immediately click my entry.
Now, if I delay any of that by even 1 second, whether because I wasn't paying attention when it spawned or due to a misclick, I end up in the instance with 9 million people.
But as said, this is anecdotal, and based on a pretty small sample size of less than 50, so there's probably more to it, and it may be due to something else entirely.