Something really weird happened and we found this:
- We ran SIS import with courses.csv and enrollment.csv
- It created a course.
- We added a teacher in manually ( not via SIS Import)
- Then ran a SIS import for student enrollment, Canvas created a Section without SIS ID and put these new students into that Section instead of the one with Instructor. The weird thing is that this new Section doesn't have SIS ID but still import enrollment.csv ( which has the Course SIS ID column) into it.
- I also manually delete the Course and run the Course.csv again with the same SIS ID I used earlier, the process said it went through, the course was created, but when I get in and search, the course is not there at all