Yea unfortunately when you have too many sprites. Especially small ones this happens. Either make the man one sprite or put all the body parts in a spritesheet. That's my advice.
This happened with my project too. Initially I wanted advance character customization so I put head eyes torso as different sprites. This is not good for rendering. Not just for Godot but other softwares too. In my case one of the eyebrow would disappear or the eyeball would disappear. Blurriness, jagged edges.