On completion of a trade round, all completed bin lifts have a transaction created. At the point of creation, a check is completed against the contract to see if the invoice frequency is advanced or in arrears.
If the contract has one of these frequencies, the transaction won't be set to invoice, as the frequency indicates to the system that these should already have been invoiced.
In cases where the contract was set this way for a period of time before being updated, which can be seen by viewing the contract and checking the field level updates tab, there may be a period where transactions weren't set to invoice.
To update these transactions:
Go to the account and click Transactions.
Click the edit button to the left of the affected transaction.
Click Create Invoice, then click Save.
Once the transactions have been updated, they're picked up in an invoice run.