IC (and sometimes ID) will often make supporting .xml files to maintain things like when folks rename the InCopy stories in the Assignments panel, or reorder the stories in Story/Galley views by dragging the story bars up and down. The files maintain those customizations for anyone else who opens the INDD file. They are innocuous and won’t harm anything if you leave them there, and if you delete them, it’ll just remove the custom settings made by the IC person.
Interesting that only 3 editors have this happening and the others don’t. Ask those users if they’ve redordered the stories in Galley/Story. Or maybe it’s some other sort of control file. I don’t know of a definitive list of these.
You could try opening the xml files in a text editor and see if the contents give you a clue as to what they’re for. If it’s reordering, it’ll be called [name of indd file] List.xml.