Friend just reported some additional issues:
I found another bug in the game. I got taken to New Bora island, killed the scyther swarm and was told to catch "any 3 native pokemon to the island" and after Gregor says "Off you go." and stops talking, I'm frozen. The music plays and a character walks around but I can't move or access the start menu or anything.
I reset to an earlier save state because I accidently caught some non-scyther before finishing off the swarm...maybe that threw it off. I'm going to try not catching any native pokemon, just a scyther as I fight them. If it still glitches I'll try not catching ANYTHING.
A less problematic glitch, when I did finish the scyther swarm off, my chara kept going "I should go back to get that Research Mission from Gregor" and moving me a couple steps automatically.... When I was already on my way back to the research base and apparently just wasn't lined up to go down the correct side of the two-tile wide stairs! This one was more of a "LOLwut" type glitch than "OH CRAP why can't I move!?" level serious.
Still froze when the only thing I caught was a scyther. So let me try just killing them all and catching nothing.
yeeeep it freezes no matter what I do.
I stopped playing with several save states, one before I went to the island, one on the island before I attack the swarm, and one where I've beaten the swarm and caught a scyther but nothing else.
I don't recall if she's playing Version 2 or Version 2.1, unfortunately.