The multiple disc badge checks apps and if you have more than one app with the disc number filled it marks it as having multiple badges
The multiple version badge checks apps and if you have more than one app that is a likely version (use emulator if base does, isn't auto before/after, obvious document file type, etc) that either DOESN'T have a disc value or has a value of 1 it is then displayed.
I'd take a look at the apps listed in game details again and see with the above information if it becomes clear why you're seeing both. If you can't get it let us know and maybe I can take some time to look through your data file to see if I can't sniff out the reason.