Multiple copies of files on SD card
This looks like the media scanner messed up its database. I recommend to:


clear the media storage (see the middle of this page for details with screenshots):


go to Settings › Apps › All
find "Media Storage" and tap the entry once to open the app details
chose "clear data" (to empty the media scanner's database)

reboot


On device startup, the media scanner will be triggered to run, and should – this time cleanly – build up it's database.

Note: If you've customized ringtones/notification/alarm sounds, you might need to redo that afterwards as the association might be lost.²



² Applications identify those sounds by an ID, not by directory and file name. With the new buildup database, those IDs no longer match.