If you use a Mac to setup RetroArch for your Wii / Wii U, be aware that OS X puts a bunch of hidden files on your SD card that can and will conflict with your RetroArch installation if you’re not careful. Be sure to remove those hidden files, specifically ones with the *.dol extension, because the Wii will attempt to load them instead of the actual boot.dol that it’s supposed to load.
If you’re comfortable with using a command line, you can navigate to your SD card and view all files–including hidden ones–by typing:
ls -a
You can remove the conflicting files by typing:
rm .*.dol
notice the leading ‘.’ before the asterisk there^. It will ensure that you don’t delete the non-hidden boot.dol that RetroArch needs.
EDIT: You can also check out the ‘easy button,’ OptimUSB and Blue Harvest apps, which will delete the hidden files for you.