On most Windows applications, if you try to close a file without saving it, the dialogue box that pops up is in the format Yes (save the file, then close) / No (don’t save the file, then close) / Cancel (don’t close):
In Atom, the dialogue box looks like Yes / Cancel / No:
[image missing due to limitation on new users]
which can lead to problems if the user habitually clicks the No or Cancel options expecting them to be in the usual place.
I don’t know what UI conventions the current layout obeys, if any, but it would be nice if the Windows version of it obeyed the Windows UI conventions.