I have a file, let's say file.txt I have done git mv file.txt to file1.txt, then I created a new file called file.txt and worked on it. Unfortunately I didn't add that file to git yet. Anyway the problem is that I did git stash, then git stash apply, but the new file.txt disappeared... anyway to get it back?
The problem here is mostly a misunderstanding of what git stash save does. It saves only changes to tracked files. Untracked files are not saved by git stash. When you moved file.txt to file1.txt, the new file.txt is an untracked file and will not be saved by git stash. This isn't a bug, it's just the way that git stash behaves. It could be that the documentation for git stash should be more clear about this.
As the documentation for git stash save states, it will do a git reset --hard after saving your changes. It was the git reset --hard that overwrote the new file.txt. One might argue that git reset --hard should generate a warning if an untracked file will be overwritten, but I still wouldn't call this a bug. It's doing what it's supposed to do.
The important thing to understand here -- and what would have saved you a lot of trouble -- is that git stash save does not save untracked files (and it probably shouldn't).