Okie dokie, took a look through and it was in fact invisible passable tiles. You see, RMXP uses three layers, and normally these are just empty spaces that won't do anything until you put something in them. But, there is a blank autotile in the upper left corner of the tileset that is used commonly as a blank space on maps, and this tends to create a problem as it is a passable space.
So, you're gonna hate me for saying this, but the best way to take care of this is to use a separate blank space (another autotile spot) that is marked as impassible, and manually place this on the third layer where you don't want the player to pass. Sounds easy, but this can be quite tedious on larger maps like yours.
I don't really know if there's any better solutions, because frankly I'm not sure WHY this happens sometimes when the blank space wasn't used. ;-;
EDIT:
You might not have set the 'passabilities' in the Database > Tab Tileset.
If you still have problems try to use a dummy tile. Make one of the tiles,
that are completely transparent, unpassable and use it to disable passability
on the map on the 3rd layer.
If you want to check the passibilty in your map, just choose some "visible"
dummy tile and fill with the bucket tool one area in the map.
A little trick to actually "see" passability/unpassability on your map.
After you finished editing just bucket it back with a passable/unpassable tile.