I'll give you a save that is well beyond that area if it still freezes then I'll upload my version of Desolation to google drive so you can download it from there.
Game.rxdata
Manaphy isn't available yet, though Phione is available in the Tourmaline Desert (Fishing or surfing don't really remember which in water area next to Mirage Tower)
Here you go, I didn't have any problems with the file so I don't know what could have caused the error. You weren't kidding about the names i see.
Game.rxdata
Are you using any mods? If you are that could have been the issue.
I would suggest downloading a clean game and starting again, since it won't be much of an issue because you are only in the beginning.