Either your disc image or your WBFS partition are corrupt. I would recommend not using WBFS anymore and check the disc image to make sure it matches the hash for it on redump.org or gametdb.com. WBFS is very flaky and has a habit of crosslinking files and trashing the entire drive.

 

I use this shell extension for checksums: http://code.kliu.org/hashcheck/

If you want to check Gamecube games there is a tool in my sig that can do that and look them up automatically. (I know you didn't mention GC but it's there if you need it. ) I was planning on adding Wii disc support to it but I haven't gotten a chance to yet.

You would need the disc image you ripped originally for it to match the redump/gametdb values because WBFS removes the unused parts of the disc and that missing data will cause it to have a different hash value. Unfortunately there is no collection of hash values for Wii games that have been converted, as far as I know.

There is a guide for converting your drive from WBFS to FAT32 if you want to do that. I believe it will tell you if any of the files on the partition are cross-linked.