Hi! Sorry for the delay, at first I did not see the link to AnswerHub with all the required details!
perhaps it is contextual, I mean, depends on the exact command you run to check-in.
I do right click on the map file on the content browser, and then “check - in”
I suspect you did a “global check in” and that may well try to check the status of all assets of your project, such as the starter content that is located in the Engine directory, outside of your project.
I am not sure of what can be done for such cases. Does Perforce or Subversion handle this case differently?