Oh, sorry, I thought the asteroids were added as childs of asteroid_spawner but now I see you add them to the spawner's parent.
But I've found your problem, it's pretty weird. For some reason, the middle asteroid is colliding with big asteroid (not the small ones weirdly). I opened middle_asteroid.tscn and big_asteroid.tscn in notepad++ and found that they had garbage values in place of collision masks and collision layers. To fix your issue, close godot, open those two files, go to the bottom and make sure you have
collision_layer = 6, and remove the line
collision_mask = ...
I don't know how they ended up with garbage values though.