I've done this a few times before with the WTW cheat. You entered the city from a point the game didn't expect you to, so it didn't fully load the area. The red code boxes are for special areas (where HMs like Cut or specific items are needed to progress), blue code boxes are just pieces of the scenery that don't have an event (like the water fountain), and the green code boxes are for portals into rooms (you know, doors.)
Sorry if you didn't need all that. I felt like pointing it out anyway. :)
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