Calculus and physics were issues for me. I was FINE in upper level courses, using and applying the principles of each, but actually passing calc 2 and physics 1 were almost impossible. I got a D+ in calc 2 (the second time around), C- in physics 1 (also round 2), and they waived physics 2 so I could graduate (I'd already taken the courses for which it was a pre-req and done well, so fortunately my dean realized it would be kind-of silly to make me take physics 2 in the summer).