I just got DU this weekend, started a new game, and I'm having this same problem. My Sim does all homework, attends all classes (& actively listens), refines & practices presentations, edits term papers until "outstanding," studies until Confident, and fails half of her classes. She is not maxed out on skills. This has happened two terms now and it's really frustrating!
I've found that the only real way to at least somewhat prevent this is to have your Sim take notes every time they attend class. It should be noted that actively listening increases skill gain, not grade gain, and if you only attend normally, you're almost guaranteed to fail. In the incident I had with the photography elective, I was having my Sim attend class normally, and he failed despite turning in an outstanding-quality paper and doing all of his homework. I don't think that should've warranted a failure. When I started having my Sims take notes every time, though, this seemed to stop happening. However, I don't think a Sim should always have to take notes in order to pass a class. In real life, even if you do poorly on a final exam, you might still get a C if the final grade is balanced out by high homework grades.
