Yes you are missing something obviously. I was referring to MacOSX trash. When you delete a file from a USB storage (DX90 is one) from a Mac it does not actually delete the files until you empty the Mac OSX trash (equivalent to Windows recycle bin). It may appear there are no files from finder but the actual space is is still occupied by the files showing up from the trash.
Do not disconnect the DX90 from Mac until you empty the trash or the files will not be deleted.