Generally, best practice is to start a new organization and classroom for each semester, which will completely avoid this error. However, we want GitHub Classroom to work for as many teacher workflows as possible, and it sounds like you have found a bug in your workflow. Could you please report this bug in the Classroom open source project?
As far as an immediate fix, I recommend creating a new organization and classroom for this semester’s assignments. With my class, I like to use a simple naming convention to ensure I can keep track of each organization and minimize the change of names being duplicates. I use
SCHOOL-COURSE-SEMESTER for each organization, so just this semester I started the organization NCAT-COMP167-Spring2019 to hold all student work from this semester. Hope this helps!