i found the exact issue that causes this bug.
this happens when the CHANNEL and UPDATE partitions are present in the ISO/WBFS. delete those in some way, and the tool will work just fine!
what i did was extract the ISO/WBFS to a folder (with --fst) using Wiimms ISO Tools (using wit copy), delete the UPDATE and CHANNEL folders, and move the files out of the DATA folder and into the root folder. i'm not sure if that last step is needed, but that's what worked for me. then just use WIT again to turn the folder back into an ISO/WBFS (both will work), and the tool should work successfully.
this happens when the CHANNEL and UPDATE partitions are present in the ISO/WBFS. delete those in some way, and the tool will work just fine!
what i did was extract the ISO/WBFS to a folder (with --fst) using Wiimms ISO Tools (using wit copy), delete the UPDATE and CHANNEL folders, and move the files out of the DATA folder and into the root folder. i'm not sure if that last step is needed, but that's what worked for me. then just use WIT again to turn the folder back into an ISO/WBFS (both will work), and the tool should work successfully.