Hi Sanaa,
1) Please check since which period you are booking cost against the WBS. I think probably Cost related to perious period might not be settled.
2) Actually if it s billing element , then Difference between the Revenue and cost should be settled to Internal Order.
3) Please check Whether Internal Order status also, whether it is allowing the settlement line items.
4) Also check whether Allocation structure is has settlement cost element for Internal order. As shown below you need to have Receiver Cat Internal order and settlement cost element.
Thanking you
Vengaiah