What is the ruling on working for a school monitoring applications company that allows payment in installments through another company that imposes late fees?

There is no objection to working for the company that produces the application which enables users to pay fees in installments and the like. This is not affected by the fact that the companies providing the service impose late penalties, because imposing penalties is impermissible. However, this has no relation to your work in producing the application, and indirect and unintentional assistance is not forbidden.