Student Enrollment on Multisite

So something a little strange that I've noticed is in how the plugin handles the student enrollment. It seems that students are enrolled in courses and that enrollment is determined by the "enrolled_course_date_2" meta key in the database being set to date. Where the 2 above is the post ID of the course.

The issue that I'm seeing is that if I'm running a multisite and a user is added to "course 2" of a sub-site, then they are also added to "course 2" on every other sub-site if those sub-sites happen to also have a course where the post ID = 2. It seems this is caused by the usermeta table being shared by every sub-site.

Is there something that I'm missing that is supposed to prevent this from happening? Currently I have the plugin installed and network activated with 3 different sub-sites that need to run their courses independent of each other. I will be using the same user store, but need to be able to control student enrollment on a site by site basis. That way a user could be a student of course 2 on one site, but not a student of course 2 on another site.

Please let me know if there is any clarification needed. I hope that I made sense.