I noticed that in my Honda Odyssey 2012, when I arrange MP3 songs by folders on a USB flash drive, the car's audio (factory built/stock head unit, not 3rd party or aftermarket) does not acknowledge the folders and play all tracks in a different order. This order is not by file name, song name, artist name or the sorting order in MP3 file meta data. The shuffle option is disabled too.
Also, each time I turn on the audio, the order of songs is changed.
On Civic 2012, I don't see this problem at all.