Is there anything special about these disks? Do they contain foreign language material, for example? Is it the same characters every time, or do they appear randomly?
One thing about the iso9660 filesystem is that the basic filenames are restricted to the old dos-like 8.3 format. But there are two forms of extensions that provide long filenames and permissions features. Windows uses the Joliet extensions, and Unix/Linux has Rock Ridge. It's possible that these extended filenames are in a different language encoding from the one you have set up as a default, or there's some problem in reading the extensions.
Take a look at the iso9660 section in the mount man page and try a few of the options there, particularly the utf8 option.
It's also possible that the disks are just corrupted in some way, such that your drive is unable to read those sectors correctly. If you can, try them out on a different system and see if they work there.