As an instructor, I always make sure I have everything needed, usually more than I have been told I will need. It sounds like you had an inexperienced instructor and guild coordinator.
I charge a flat fee, based on the class difficulty, anything over that goes to the guild. I also do not surcharge on any items I provide for the class, only the price of the item.
I agree with Sue, that the class size should be limited to what the instructor indicates so that there is enough time for everyone. Very often the level of experience varies greatly in classes, some students require more help than others. I usually remain after for any followup questions, and offer after class assistance through my email and even invite the ladies to come to my studio and work on their quilt, no charge.
I believe that if someone pays for a class, they are entitled to a finished quilt. Very often class times are so limited, and so much has to be gone over, there is never enough time to finish.
I want to see a finished quilt for all my students! My studio is always open to all students to work on any quilt that they have signed up for a class here.