A red ! means that the file is different that the main branch. Nothing to worry about, because all files in the user settings are used to save your BUG configuration. It just means that your BUG configuration is a little different than the default one from the main branch. Although it is kinda weird that it is Bug Core.ini. I would expect the other files to be changed for customizing your BUG settings. To see what is changed, you can right-click on the file with the red !, TortoiseGit->diff.