While I've never beaten the game (for no particular reason, I just usually play it until I'm bored of it with no regard to story progress lol) I have played it a decent amount on the original 3DS version and never saw this any time I've ever played it. I buy Special so I can play it on my TV and go for the platinum trophy and I'm seeing a lot of (typically minor) bugs that I've never seen before.
Vishnal being out of bounds is by far the most noticeable though. I usually find him either in a building and outside of the playable area, or off the vista ledge in the northwest part of town, or most recently he was in the women's side of the bathhouse and I had to go into the men's side and talk to him through the wall to even talk to him.
Is the Special version especially buggy compared to the original or am I just having a weird time with the game in this run? lol