It is very odd. The course does not matter, as you said you already completed the required courses. It may be a misunderstanding. I don't know if you can do the flagpoling or not. But you can do a research on it, if you can go to border, you can easily explain and get your permit.I did. They all received their work permits without any issue. The only difference was that I had dropped a course in the January 2021 term. Since I had already completed the required courses, I dropped a non essential course since it was interfering with my research. The course showed up with the status "withdrawn" on my transcript. They had never taken up any additional course.