Very bold claim you make there without reproducing it and showing video proof.
I have personally used generic flash drives (PNY, Kingston, SanDisk), failing 2.5'' and 3.5 hard drives through cheapo no-name usb to sata adapters, generic micro SD with USB adapter, branded micro SD with USB adapter (Samsung, SanDisk, PNY), not a single corruption ever with any emulator, specially WiiSXRX, whether on loading or saving settings. Ever. And boy oh boy have i obliterated all that media with tests, copying and writing.
Sadly, your USB drive is almost 98% sure crap, probably one of those rare cases of not being 100% compatible with the Wii, or suffering from a bad partition from before, who knows. Use a good partition software, and try to start fresh. Otherwise change to another brand.
I have a 1GB generic SD card that came with my SD Media Launcher, from 2006ish. Still alive after who knows how much media writes with games and emulators.