In Elly's mission, when going to the basement of the church, a lag occurs that makes the mission impossible to complete, after a while the game freezes and crashes making it impossible to recruit Elly.

I don't know if other areas of the game have this problem (But from what I read looking for a solution it seems so) since I started a new game.

I have the game on Steam and I left a post stating the problem there too, but I think that through itch.io the contact is more "direct"

Yeah, same for me, freezes. I don't take other chests cause of freezing. 

The same thing in Lielle's Dungeon, you can't even move, so I use riddle key