Setup and Operation (expense items) is independent of contracts — the expense items represent ongoing costs that are not tied to one specific agreement.
If you want to distribute costs per contract (e.g. because you have several agreements or suppliers linked to the same type of cost), you should use the Payment Plan on the contract instead of Setup and Operation. This prevents the cost from being counted twice (both as an expense item and as a contract cost).
If the contract has no Payment Plan, you can still accrue it. See Accrue a contract without a Payment Plan.
Rule of thumb: expense items for ongoing, non-contract costs — the Payment Plan on the contract when the cost is tied to a specific supplier agreement. Read more about expense items in Setup and Operation.