For this case the solution is, simply add dot next to it:
git clone [email protected]:user/my-project.git .
Even then the error doesn’t resolve to make sure that the directory is empty if you are not sure about your directory then run the above command with:
rm -rf .* && git clone ssh://[email protected]/home/user/private/repos/project_hub.git .
This will remove the files present in the directory and then it works.