Here are two ways to unstage individual staged file using Git GUI.
Select individual file under “Staged Changes” which you want to stage. You may use Shift or Ctrl keys to select those files. Once selected, click on “Commit” menu and select “Unstage From Commit”
It will stage the selected files
Click on individual file icon in “Staged Changes”. Make sure you click on icon and not on the file name. Otherwise it will not work.
It will stage the clicked file