Trouble comes from when one's file system is displayed on the other...
It's as easy to say that PC's are the same, because when their file systems get displayed on a Mac, THEIR housekeeping invisible files get displayed, too.
Neither is at fault, basically, as long as you stick to one system or the other. The problem comes when you take something out of one, and put it into hardware based around the file system of the other (as the OP has).
_________________________
An arranger is just a tool. What matters is what you build with it..!