Welcome to all to many of the courses that you're likely to have. Unfortunately that's just the way that it goes; particularly the first year or two. I had to go to school an entire extra semester to retake classes that I "Failed" due to attendance even though I had an "A" and often even the highest, grade in the entire class.
If you do wish to file some sort of complaint, I would simply start with either the Department head or, if you get nothing there, the Dean/Chair of your College/School (assuming you have multipe colleges in your university, I don't mean the head guy of your entire university). A Department head is much more likely to be receptive of your concerns and actually in a place to do something about it.
