Говно (ошибка ):
Dictionary <int, Projectile> ProjectileTypes { get; set; }
public int CurrentProjectileId { get; set; }

public override void _Ready()
{
    ProjectileTypes = new Dictionary<int, Projectile>()
        {
            {1, (Fireball)FireballScene.Instantiate()},
            {2, (Iceball)IceballScene.Instantiate()}
        };
    CurrentProjectileId = 1;
    Shoot();
}

public void Shoot()
{
//Когда стреляю второй раз одним и тем же прожектайлом - Unable to cast object of type 'Godot.GodotObject' to type 'Game.Models.Projectile'.
    Projectile projectileInstance = ProjectileTypes[CurrentProjectileId];
    projectileInstance.DoSomething();
}

Норм:
public void Shoot()
{
    Projectile projectileInstance = null;
        switch (CurrentProjectileId)
        {
            case 1:
                projectileInstance = (Fireball)FireballScene.Instantiate();
                break;
            case 2:
                projectileInstance = (Iceball)IceballScene.Instantiate();
                break;
            default:
                break;
        }
    projectileInstance.DoSomething();
}