You are scaling the whole player. Scaling collision shapes causes glitches with the physics engine (they should never be scaled).
What you want to do is only scale the visual appearance of the sprites, none of the other objects. Since you have different parts of the body on different layers, what you might want to do is create a parent object and put only the body parts in that. It could be just a Node2D or maybe a CanvasGroup if you wish to do any coloring or transparency. You'll have to edit the animation though since it will break the links.
https://docs.godotengine.org/en/stable/classes/class_canvasgroup.html