Yup, thats normal.
Commercial software was largely copy protected by Rob Northen Computing (he copy protected around 500 Amiga games).
Workbench will recognise protected disks as "NDOS", "PDOS" or "MDOS". However it will not be able to read the disk because it uses a format not recognised by WB.
Look for a disk copying utility (such as Disk Copy), preferably with dongle, and that should be able to copy the disk for you. It will copy the data across exactly as read from the source disk and you should be able to use your copy in exactly the same way as the original.
I haven't backed up any of my games yet, but I did make a back-up copy of Simply A State Of The Art - an awesome graphical demo

Regards,
Lonewolf10