If either Emi (probably Kiri as well, but untested) is defeated during the boss battle against the golems in the cave in Elkia forest but you win the battle, that character becomes permanently locked out. They follow you normally as you travel around, but in combat they show up as if they are captured by a golem, regardless of where you are or what you are fighting. I tried sleeping, talking to Aya, getting party wiped by different enemies, nothing worked. Eventually had to reload a previous save and lose ~1 hour of progress. Not sure if this also happens with other boss enemies as well.
Viewing post in Post bugs here (version 1.31 onwards)
I tried being defeated by the plants in the forest, the puppets, and the bandits in the Old Mine, then searching the rescue locations. In each case, there was nothing in the spot I was supposed to find Emi, since she was still following me. If I got into combat Emi would have the "defeated by Golem" image and would be unable to do actions. I just reloaded a previous save. Enjoying the game! Really wish this and some of the others were available on Steam as well.