Glitch elaboration, mostly spoiler-free
Like in most RPGs, there are a few optional events throughout the game, that you can trigger whenever you go to the right place or talk to the right person. It turns out they expected you to have finished some specific ones of these events by the time you get a late-game party member, so if said character is in your party when you enter one of them, the cutscene handler doesn't know what to do with them and essentially erases them from existence, making it impossible to have four party members, which apparently breaks a cutscene that happens during the final battle, as it's not supposed to be possible to have only three characters in your party after a certain point.
re: Glitch elaboration, mostly spoiler-free
The only method the game has of changing party members goes through two steps: talk to the party member you want to join, then select one of your existing party members to replace. It's not possible to skip the replacement step, so even though the lost character does return to the place you go to change party members, you can never again have a four-member party.