So, I tested it out, and I COULD get it to do the same thing during the purple sphere cut scene. Depending on which party you start as when you try to bring down the barrier you either
A: teleport to the purple sphere at the start of the cut scene, causing it to play out wrong (No MECHANICAL problem here, but it is a rather large graphical glitch)
or B: You start the cutscene as Varia's group. A minor issue, except that this means that when you are dumped into the menu, unless you add him to the party, you can actually start the boss fight without Simon in the party. He is supposed to be required, but I guess it doesn't check to see if he was somehow removed since it is assumed you will be starting as his group. Visually works fine, but mechanically broke AF.
It looks like you can actually trigger this bug at several points. Basically, if there isn't text on the screen, even for a split second, you can trigger it. Like when you get confronted by the enemies at the entrance, there is a moment when your character does the ! symbol; you can do it at that moment, too. I was actually able to combine both bugs A and B together by triggering the transition multiple times after using the sphere. After finding that out, I went through and checked a bunch of other dialogues from this section. I was able to trigger the party switch while Uyae is unlocking the puzzle door, and when the screen darkened while collecting the Divine Claw Charm. Given the party doesn't move during these scenes, there really isn't any problem with that, mechanically, but I could still DO it. I have a feeling this is going to be a problem, or at least present, in damn near every multi-party section of the game. I will check the Incubus King's Castle when I get there in this run.
Saving and Loading resets the positions correctly, but not the party composition. See attached save for a no Simon party.
Oh, and on an unrelated note, durring Terri's scene (The Ivalan Succubus) during the Third Arclant War, its possible to get an odd situation; when transfering from Ferholm to Stienford, Simon and Sho are are simply added to the party. Simon gets slotted into the second spot, meaning he wont be the party leader on the map by default; that will be Robin. I thought it would be a little funny to put Sho as the first slot, so it would be her sprite running around.
Well, when Terri's scene is over, Terri will be in the room with whoever is the party leader's sprite. Which in my case, was Sho. Nothing mechanically broken there, just a funny situation that yall might want to fix, because while Simon's sprite would make the most sense there, and I could conceivably see Robin nearby, I cannot image any reason for Sho to be in the room for a succubus blowjob. See attached save from just before the Terri scene.
https://ufile.io/f/8fk6k