How to Instantiate prefab in specified scene？

My English is not good，sorry for that
I have multiple scenes at the same time.
I want to Instantiate prefab in the specified scene.
Now it's only appears on the top.

I have a manager scene for managing other scenes, and a level scene is loaded with SceneManager.LoadScene() , both scenes exist at the same time.
The script in the level scene instantiates a prefab with Instantiate() and finds that the instantiated object appears in the manager scene!

I can only temporarily move it to the level scene with SceneManager.MoveGameObjectToScene() .

Is there a way to specify an instantiated scene for the prefab?

What shall I do?