Salary Sacrifice deductions are pre-tax deductions that are sent to a super fund. First thing to check is they should be set to superfund, common mistakes is they are set as manual payment. Assigning a "Salary Sacrifice" deduction to a "Manual payment" the system will not view this as a super deduction but instead as a basic pre-tax deduction that you take from the employees wages for an undisclosed reason outside of the system. Because it views it as an undisclosed deduction it won't be included in your RESC in STP.
If you are using Beam for automated Super Payments, you will need to manually exclude these contributions from your batch if you have manually paid it.