Prefabs getting deleted in all scenes!

So I was working on a Level on Unity. Basically in the game a cube (player) has to avoid obstacles and go to the end point. After all the coding and everything I wanted to make 3 levels with increasing difficulty. So i duplicated the scene and when I deleted some of the obstacles (which are prefabs) in "Level 1" it effected the other levels and deleted them all. If i add obstacles it also effects all levels. I wanna know what I can do stop that. I followed the video tutorial of "Brackeys" from YouTube, he didn't seem to have that issue.