Most of the courses have 3-4 modules that are spread out over 4 Levels. It's very possible that you have fully completed only a module for a particular course which is why it's not showing 100% Completed.
Recall that new material is released every 30 days—if you've completed a challenge. (The idea is to practice using the tools otherwise, doing things like the Do-Overs or the transference exercises (for Better Therapy members) won't work. You need to be solidly in right-brain mode for them to work otherwise your left "thinking" brain will interfere. You can see all the modules for different courses in your Roadmap.
Here's an example of the Science of Serenity with all the modules listed: https://myshrink.com/wp-content/uploads/Science-of-Serenity.png If you still feel there's a problem, let us know.