In my Xcode I can see two projects source "Source control navigator" option as below,

And so if I make commits from Xcode I am getting the changes list in both the projects.
Note:
- I am using source tree for GIT operations,
- I have tried removing and adding the project freshly again the same issue occurs,
- In source tree only one project is shown and no issue in that.
- But in the "Project navigator" I am seeing only one project as shown below.

I want to know what could be the issue and why this occurs and how to rectify it?