That is so weird. I didn't even know it was possible to overwrite the original movie.
I don't know what you mean by apply button though. Where do you see that at?
I always hit done, and then from there it's only saved in iMovie. You can export it to you camera roll from there, or YouTube, etc, but you have to tell it to do it, it doesn't do it automatically. When you click to export it to camera roll, it's an all new video, and the original is still there in the camera roll as well.