I was going to ask if you did something or missed something and got yourself stuck, so I tried to deliberately get myself stuck.
First, I tried using Phoenix Dive to get the second pyramid before the first, but all that happened was that Zixzax just gave me the first one anyway. I didn't get stuck.
Second, I deliberately avoided all the waypoints before entering the Shelter Plane, but one was unlocked for me anyway. I didn't get stuck.
So unfortunately, I don't know the cause of why you got stuck, and can't offer suggestions of how to get out. Unless... did you use the button with one of your party members dead? I've heard that you can get stuck that way.
