Answer for people who has same problem.

In my case I changed some of my files name to capitalize version. The problem was Git didn't resolve this change that's why my file structure was wrong on Github. So Solution is changind this config with git.

git config core.ignorecase false this command makes git to be aware of capitalization.

Here is another question on Stacoverflow: I change the capitalization of a directory and Git doesn't seem to pick up on it