Cell Permission Limiter
Cell Permission Limiter
Just reset the protections on the sheet using the add-on menu, then add in your additional columns and run 'Set Protections' again.
The add-on has quite a complicated job to do to set the permissions of each row in your spreadsheet. The more users you add, the longer it will take. That said, it is still much quicker than trying to do it manually. It is completely normal for the add-on to take a few minutes to do a class of 30 students.
This happens if there was an issue with sharing the spreadsheet with that user, it may be that the email address was typed incorrectly or some other error occurred.