After helping undergraduates for many years, I think there are several reasons:
1) To really understand it, you have to remember material that is taught in the first half of the course. The material is inherently cumulative. This is difficult if you are used to classes where each exam is testing an isolated set of topics. In some courses, this early material is taught poorly, or not emphasized enough (e.g. skeletal structures, acid/base chemistry, resonance, etc). Understanding this early material does require a certain amount of independent thought on the student's part, which can be different from other classes where one is simply expected to regurgitate facts.
2) The material is much more visually based than other courses. If you are better at remembering everything as a series of words, it can be difficult to change this mindset. When students are first learning the material, it's extremely difficult to remember all the words associated with each process, but remembering all the words is not actually necessary for exams. Professors may use all the proper terminology when teaching, and fail to emphasize important points as a result. Again, some responsibility also falls on the student to attempt some independent analysis.
3) The organization of many textbooks is less than ideal. The material is sometimes presented as a list of random facts, instead of taught as a cohesive whole. If too many separate topics are brought up too soon, it can be difficult to learn patterns and build up intuition. Textbooks should avoid bringing up poorly explained experimental results whenever possible.