You are trying to use feature what is not supported by physics engine.I remember there was one bool in rigidbody 3D properties what was not supported. If i remember right, enabling custom integrator on rigidbody was causing this. It is not somehow important, it just telling you that feature you are calling is not supported so this specific feature will not work. You can safely ignore it, it not going to crash your computer and you cannot fix it from inside Godot because it is bug in physics engine.
Also, you should do 2D game. GoDot is very immature in 3D and it will take some time than 3D will be fully usable. It is usable but 3D have long list of bugs. There was discussion about that : Godot 3D lack of polish(forum discussion)
Garrom out.