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So how do you get them? When I first walked into the cave Cherren takes you in, I noticed some dirt being tossed around and did find the mole Pokémon there. It has been the only time I had this happening, and I'm at my 4th badge already. I have some questions, I hope someone already did some research on the matter:
1) Will they appear randomly, also when you are standing still, or do you need to (re-)enter the area? 2) Will they dissappear whenever they appear? Like, do you quickly have to make your way there before it dissappears? Will it dissappear when you get attacked by another wild Pokemon?
They appear to be randomly occurring and will stay in place until a scene change such as a battle. Repel will not prevent you from getting into a battle on that square. I've encountered the grass shaking, rumbling earth in caves and water puddles, but have yet to see the bridge shadows. If you use a repel and listen carefully, you should hear another sound effect when you're standing still, that's when you know it's happening.
Just to let you know, every time you take a step, there is a small percent chance that a rare Pokémon spot (like rustling grass) will appear on-screen within five or so spaces of the player. This means that there is an element of randomness toward finding one, but they generally don't take too long to show up if you just run back and forth next to some tall grass. Note that you can open the menu, switch your Pokémon around, save your progress, and do other things like that without the spot disappearing; I think that entering a battle is the only thing that makes one disappear. Also, the Pokémon that you find in these spots vary depending on where you are, so check them in lots of different places. Tabunne can be found easily in rustling grass in any area (and gives tons of experience), but you can also find the three monkeys in the big forest near the second gym (they're common), and many areas have evolved forms that can be found through this method (but very rarely). Also, in the area where you find Nageki or Dageki depending on the version, you can find the other one in rustling grass, but only rarely.
Oh, and I'm pretty sure there aren't any rare spots in the desert.