The leave type has been set to Calendar Days in Leave Setup --> Leave Type.
In order to rectify it, Calendar Days must be changed to Working Days. The weekends/public holidays will not be deducted as leave.
If the system is just counting weekends when staff applied for leave, it could be due to the work week assigned to them.
Check in eLeave > Leave Setup for the work weeks setup and ensure that each staff is assigned the correct work week under Leave Admin > Set Entitlement.