To reproduce:
1. Open the attached project
2. Run the scene
3. (De)select the Cube prefab from the Project View
4. Notice that the size of the returned FindGameObjectsWithTag() array is increased as you select the prefab and decreased as you deselect the prefab.

This is expected in the editor as GameObject.FindGameObjectsWithTag does not do any filtering. If you want to filter the prefab object you can check if the GameObject is persistent https://docs.unity3d.com/ScriptReference/EditorUtility.IsPersistent.html