If you split an order and two different shipments go out for it (For example Part 1 goes with Royal Mail and Part 2 goes with Hermes) or you have multiple parcels so multiple labels are generated, this will produce two separate tracking numbers.
You can use the Despatch Report (Reports next Overview then DespatchReport) to view this data, It will show you the various parts of the order.
Note: If you split an order each part will have a Despatch Note as well to see this data.