Is there a special status awarded to the plants (shrubs?) growing out of the Kotel? Why don't they get rid of them, as their roots obviously have deleterious effects on the wall?
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The Mishna on Megilla 28a rules that a destroyed synagogue retains holiness, and if grasses grew on it they should not be picked because they add to the feeling of despair. (The subsequent Gemara on 29b discusses picking the grasses and leaving them there, though the Rambam (Perush HaMishna 3:4) and the Mishna Berura (OC 151 sk 29) both understand this to be optional.)
Though the Kotel is not a destroyed anything, I think similar logic may apply.
The relevant part of the Mishna:
It could be that pulling them out would cause direct damage to the wall, while leaving them there is only indirectly causing damage, and that we prefer the former.