I had 4-5 games do that in a single go, but I used WBM only to copy to WBFS partition.
The ones that failed, I simply removed of the list, re-ripped & converted to WBFS files, & all was good to go.
In my case, it was due to old/bad rips, but I never got booted out of WBM.
The invalid games aren't easily identified, so you need to tick/mark the games that succeeded & then compare with your intended games. Then you will know which witch is which
Have you tried simply copying your WBFS files directly through Windows ? That's how I did my HDD's using Fat32. All good there too. I used WiiBaFu to dump & convert.