Well, thats just about the only idea I had, so if it can't be figured out, you can try covering them up. You said before that putting invisible events on them can make tiles unpassable, so I suggest that
*make the lake in Forest of Feeling smaller by putting more trees on the sides(and events into the trees just to be sure)
*put a tree on the tiles in Aliora Meadow and Gym so that passability would not be a bug but a feature
*recreate the legend dairy house from scratch(it looks like a small map, so might not take too long?)