Is it generally worth the time and effort to challenge incorrect exam test items? Background information:

I have just finished refreshing my high school courses in order to enter into university for engineering. Because I have a strong desire to become an engineer I have not moved past any material unless I fully understood it. That being said, the courses I took have had many mistakes in the material (online material as this is through online correspondence). I have had to fight tooth and nail to correct some of the material, even though I was a student, because I believe the material should be correct so that future students do not suffer the same frustration nor are taught improper concepts. 

An example to convey the level of quality of the course material:

One example was in the Physics course, the concept of work being taught was equal to force times the distance the object traveled. This is fundamentally wrong; the real concept of work is force times the distance the force was applied over. I wrote to many people and eventually the business owner before my concerns were heard. The only reason I knew this was wrong was because it defied the law of conservation of energy. Though the fact that I, a student, was the only person who realized the mistake and sought to have it fixed reflects very poorly on the quality of the institution. 

Strictly relevant to my question:

I have gotten into the habit of contesting test questions which are incorrect, and since every question on the final exam is worth 0.66% of my final grade, I take the time to make sure each mistake was mine. After contesting 2 questions on my last Chemistry final exam I have found that the head of the science department (whom I correspond with) does not understand a specific concept regarding a question. Now, I realize that it is only 1 question and my grade will go from a 97 to a 97.6, but I strongly dislike the idea of losing a mark for a concept which I deserve the acknowledgment of understanding (the grade). In order to explain why my answer was correct, I don't know how to do it in a way that is not condescending towards her (the head of the science department); no matter how you look at it, it will be a student explaining a concept to a teacher.

I am asking for criticism here. Please criticize me and tell me if I am being too much of a perfectionist. Is it appropriate to always contest questions during an academic career or will it have a negative effect on my success in the long run? Also, is it really worth it? What are the pros and cons? 

EDIT: I can see my comment about the Physics concept of work is being met with a lot of skepticism; so I am including the link to the Physics.SE question I made in order to verify without a doubt that the lesson was indeed incorrect. When I saw that this was a mistake I took every measure that I could to ensure it was in fact a mistake before I proceeded to contact the head of the science department and then the business owner (when my concerns were not being heard). In no way did I take this lightly and assume I was correct, I did the necessary research before raising concerns.
Though the fact that I, a student, was the only person who realized the mistake and sought to have it fixed reflects very poorly on the quality of the institution. 


Yes, it does.  


  I believe the material should be correct so that future students do not suffer the same frustration nor are taught improper concepts. 


Of course it should.  But ultimately, the correctness of the course material is the responsibility of the instructor, not your responsibility.  


  I have had to fight tooth and nail to correct some of the material.


That strikes me as quixotic.

It's certainly reasonable, and helpful to future students, to report errors that you find in the course material.  The instructor should then either fix it, or discuss with you why the course material is actually correct.

But if the instructor does not seem interested in doing so, then it's probably a waste of your time to "fight tooth and nail".  Unfortunately, crappy courses and instructors exist, and it's not your job to fix them all.  Simply quit giving them your money and attention: look elsewhere for better courses.  If you like, leave negative reviews.  Future students would be helped by having the errors fixed, but if the courses are as poorly managed as you describe, they would be even better off not taking them at all.