So after 2 days and 3 hours on the phone with Apple Care I have found a solution. I had restarted, logged out of icould, and even reset to factory default and shows were still not updating in the up-next que.
What I had to do is go into settings, apps, TV, Home Screen. Change from up next to what to watch. Then go to app switcher and close all of the apps. Go back to the settings and change from what to watch back to up next. Then my up next que started updating again.
So I hope apple care updates their support documentation because support said it seems like a bug to her. I hope this solution helps someone else in the future.