This is most likely to have occurred as the result of stock not being available and / or allocated to the order when the first invoice was generated. You would have manually had to select Release from the Actions menu within [Sales Invoice Manager | Awaiting Stock] for the system to have sent the incomplete order for despatch. One invoice would be raised for this part of the order.

The part-shipped sales order would be placed in Awaiting Stock waiting for the remainder of the items to be booked in. As soon as stock became available for the items not initially despatched, the system would have allocated them to the order and released the remainder of the order for despatch.

If you do not buy the products in question, such as labour charges, please see the guide here: Items with Zero Value on Sales Orders within Sales Invoice Manager