I had a similar problem to you, but it was inside Yet Another Wad Manager Mod.
I'm going to walk you through discovering something.

1) Open the terminal program (open the app screen - F4 (or Fn+F4 if you change your special key settings))
2) Navigate to the rom folder on your SD Card (type "cd " and then drag your roms folder onto the Terminal window, then press Enter - don't forget that spacebar)
3) Type "ls". You should see all of your roms in there.
4) Type "sudo ls" You will be asked for an administrator password. Enter it. (Nothing will appear on your screen as you type your password, but it is indeed being typed.)
5) You will notice all of these files starting with the name "._"!

These files are left over by Finder when you copy files. These files contain extra metadata that cannot be embedded into FAT32 file systems, but is necessary for Finder to organise the files properly. Don't worry, it is perfectly safe to delete these files. And you can do it with one command.

6) Type "sudo rm ._*"
7) Type "sudo ls" again, all the ._ files should be gone.
8) Type "logout" and close the Terminal. Eject tour SD Card.
9) Re-insert your SD Card into your Wii U and (hopefully) enjoy your SNES emulation!

 

Double post with updated info on my findings.

None of my emulators or homebrew will run games now. They load but give me the same errors as I described earlier.

I went ahead and did what you reccommended and it did manage to delete those files but I also found more of them lurking all over and I have way too many folders on that card and I'm a bit lazy when it comes to going over every single folder on it.

Is there a way or command that will delete all those kind of files on the card?

Thanks again!

 

Ok. That did it. Gone!

Everything works now. Thanks!