I once worked for a Yeshiva with low fees and loads of non serious people applied just to
a- give their child the experience of going through the interview process and
b- keep their options open.
It cost me mega hours of research and interview time. Once we raised the fees we pared it down to those who were seriously considering our mossad and life became more focused and productive. We were also seen in the eyes of the public as a more serious place than when we charged mush less. We DID deduct the fee from the tuition for those accepted.
What I have difficulty understanding is why my local elementary and high school charge a yearly registration fee of 200 dollars for a child who is already enrolled! What is the justification?