Using sourcetree 3.3.8. Select a file in unstaged files area, perform an external diff, perform a change to the file and save it. In my case, i used winmerge, which creates a .bak file after saving. When closing the external merge tool, you can see the additional .bak file appear in the unstaged area. Now, right click and press Remove on the .bak file. In the dialog that appears now, you will see 2 files to be deleted which is incorrect.