If you connect one or more usb stick with roms ((unmounted)) the system automatically make a backup of the rute and roms you have in flash drive to access more quickly and this files have your disk space (if you unplug the usb stick you see the same roms tittles on emulators for this files reason)
Solution:
1-If you connect the raspberry with wifi use WINSCP to access to the files and dellete the files in the rom folder of internal raspberry memory ((remenber this files are only shortcut you can dellete then for free space on disk))
2-If you dont have wifi install new image of retropie (and remenber if you connect usb stick unmounted the system make a shortcut backup

Sorry for bad english but I try! ;)