Ugh, the sims 4 university grades are so glitchy, I totally feel your frustration. I’m a student and currently taking digital media and game design, so I play sims to de stress, but sometimes the game's grading system is more stressful than my actual finals.
I had the same issue where the exam schedule didn't align with my end term. It made me so paranoid about my real grades that I started using the grade calculator. In the game, a B is annoying, but in my real degree, I need to know exactly what I need on my finals to keep my GPA up.
For your sim, try to email professors about progress right before the term ends, it sometimes forces the game to update the grade correctly. But for real-life peace of mind, I definitely recommend using a tracker. it takes the sims-level guesswork out of your actual GPA.