Notice: This bug has been fixed, I am posting it for the sake that no others will do also.
You cannot re-enter the harbor in Vermillion City unless a portion of the roof is visible on-screen (so you can't enter in 1st person, and some of 3rd person mode).
You cannot re-enter the harbor in Vermillion City unless a portion of the roof is visible on-screen (so you can't enter in 1st person, and some of 3rd person mode).