GITLAB branch compare detect all files as difference in two branch


I have some issue with my gitlab. I have two server, one is production, and one is development. Before using gitlab, we use FTP to deploy between server. And then, we use GIT. So I make two branch with those two server, master branch contains all the script from our production server, and dev branch contains all the script from our development server.

And then, I tried to compare the difference between two branch, and turns out, all the files is different between two server. Not just different, Gitlab is marking all the file as a new file. Does this normal?

Oh, and I tried to make new branch using master branch, add 1 new file, and compare using the same method, it works. Gitlab only detect 1 new file, instead of all the files like the issue I address before. Can anyone help me?