When copying a Canvas course the groups do not copy correctly.
For example, if a course has 3 group sets, when you copy the course it will merge those into one new group set with the name "Project Groups". It then also takes any group assignments/discussions and links them to that one new group set, even if they were linking to different group sets. For example, if I have a group set for discussions, and one for the final group project, Canvas will create one new group set of "project groups" and all the assignments and discussions then link to that one new group set. So after copying a course you need to create the groups and then go through all the assignments and discussions and re-link them to the correct group set.
When copying a course copy over the group sets and link the assignments/discussions to those same group sets. So if I have a course with a discussion and final project group set, create those same group sets and link the assignments/discussions to the same group sets as where you are copying from.
Added to Theme
Simplify bulk course tasks Theme Status: Identified