After recruiting the last party member and having Team Nineball rejoin, party member number 2 is locked and the next random encounter is inescapable. This is fixed after the battle finishes.
Happened on all routes.
Viewing post in Touhou - Grimoire of The Elemental Castle comments
Right. This one is somewhat necessary.
The scripts used will crash the game if you recruit a new member and not use him/her at least once in a battle immediately.
For example, if you recruit Lily but not add her to formation and battle with her in the party in the very next battle encounter, the game will crash right after.
Some characters like Daiyousei joins right before a boss encounter, so you won't notice that she's actually also fixed in her position.
Unfortunately, I found this bug in the script late in development, so it's a bit too late to change everyone's first battle into a boss encounter of some sorts.
Since I am not skilled enough to alter the game scripts, and the one who originally wrote the scripts has left the RPG Maker community AFAIK, this is the only workaround I've discovered and can reasonably use.
Sorry for the inconvenience.