Welcome to the forums @oulibha!
I think it is probably a bug. I would suggest making an issue on GitHub for this issue, if there is not one already.
What is probably happening is that the PhysicsBone node doesn't clear the global_pose_override
when it is stopped, which causes the bones to always take the overridden position. If this is the case, you can work around the issue by calling set_global_pose_override(bone_id, Transform(), 0.0, false)
on each bone affected by physics, which should clear the physics override.