SchoolLogic 4.5 and older. May also affect newer versions.
Despite the choices you set up in SchoolLogic Preferences, when a Student withdraws from a Class, the software doesn't automatically remove Fees associated with that Class.
When Scheduling staff remove a student from a Class which they know, or believe, charges fee(s), they should check that Student's Individual Fees and Payments form on the Fees menu. Click the red x next to the class in question. That should immediately remove that line from the upper part of this form and automatically change the total which the Student owes. Be sure to verify the latter.