Usually these waiting lists are maintained only by the registrar. As a result, the individual instructor does not have the discretion to determine who gets into his/her class. This policy is intended to avoid the favoritism and arbitrariness that you have experienced. One exception may be if there are prerequisites for a class, and the instructor has the discretion to determine whether or not a student, including wait-listed students, have the necessary prerequisites.
See www.higheredjustice.com.