Take a course and modify the permissions of a block within that course, removing the Authenticated user and/or Guest roles from the block. Backup and restore the course. In the restored course, the block which was modified in the original course now has the Authenticated user and/or Guest roles added back.
To replicate, as an administrator perform the following steps:
1. Create a course; turn editing on
2. Add a block to the course (HTML block is a good example)
3. Click "Assign roles in block"
4. In the block's Administration block, click "Permissions"
5. For "View block" remove either (or both) Guest and/or Authenticated user roles.
6. Backup the course without users; all other backup settings take the default
7. Restore this backup to a new course; take all defaults
8. During the restore, on the "6. Process" page, depending on which role(s) were removed in step 5 above, you'll receive the message that "The [role] in the backup file cannot be mapped to any of the roles that you are allowed to assign." You'll also get a "Restore role mappings dialog". The "Guest" and/or "Authenticated user" roles have default roles of "None" for mappings.
9. Click Continue
10. Navigate to the restored block for which you altered the role permissions in step 5 above. Note that the removed role(s) have been added to the block.
The expected behavior is that whatever roles were removed from a block in an original course should not appear in the restored course.