If the meal account in Admin > Meals > Student Meal Payments is showing that a student eligible for Free School Meals (FSM) is being billed for meals, then go onto the student's extended tab on their profile, scroll down to Further Information and click Manage next to Is X eligible for free meals? Make sure the box is ticked to say that they are claiming free school meals, then click Update.
Another reason for the meal charges may be due to the FSM period being entered on the student's extended tab after a meal pattern was set up for the student, so all meals will have been assigned as charged. You can go to Admin > Meals > Bulk Student Lunches, select the students' year/form, and then reassign the meal pattern from today, which will make them free meals. For any date prior to this, you will need to go to Admin > Meals > Individual Student Lunches, enter the dates and the student name, then de-select and reasign each meal so that it will be non-charged.