您没有更新日志中打印的值。
position变量只保存预置件示例化时的世界位置。
下面是一个基于您的代码的基本脚本，它给出了您所期望的世界位置。
下面，spherePrefab是一个3D游戏对象球体，我只添加了一个带有默认参数的刚体。
用例如下所示：按下鼠标按钮，然后观察Unity控制台。

using UnityEngine;

public class Test : MonoBehaviour
{
    [SerializeField] GameObject spherePrefab;

    const float SPEED = 2f;

    // Initialization
    Vector3 _sphere_position = Vector3.zero;
    bool _display_log = false;
    GameObject _sphere_ref = null;

    void Update()
    {
        if (Input.GetMouseButtonDown(0))
        {
            Vector3 direction = new(Random.Range(-1.0f, 1.0f), Random.Range(-1.0f, 1.0f), Random.Range(-1.0f, 1.0f));

            _sphere_ref = Instantiate(spherePrefab, transform.position, Quaternion.identity);
            _sphere_ref.GetComponent<Rigidbody>().velocity = direction * SPEED; // this moves the object randomly
            _sphere_position = _sphere_ref.transform.position;

            Debug.Log(_sphere_position); // This prints the spawners location every frame but no the spheres.

            _display_log = true;
        }

        // This case is expected to be entered after setting sphere_ref in order not to be null
        if (_display_log)
        {
            // Update the value
            _sphere_position = _sphere_ref.transform.position;

            // Print it
            Debug.Log(_sphere_position);
        }
    }
}