The 'old weathered temple' and 'abandoned grove hideout' dungeons as part of Lilia: Temptations also kick the player out.
As does the second dungeon in Kuro's disappearance quest.
After the arena battle with Greg, when talking with Rouge, when she's supposed to say the player's name, she instead says [NAME].
The rebel base dungeon in 'Proof of Loyalty' also kicks you out without letting you collect rewards or captured slaves.
The final dungeon in Kuro's 'Apostasy' quest also kicks you out. And the Nyx item drop reads "ITEMNYX_HEADGEAR" rather than its actual name.