Hey Jonathan,
Do you have a more specific example? In ecoinvent, there is costs inside each reference product. Be aware that these costs are only for allocation purposes, for hotspots screenings or very rough estimates. The prices from ecoinvent are only per flow and not per exchange, so you will find e.g. the same price for electricity in the whole world.
Technically, openLCA will calculate the costs from inputs and outputs of all processes in the product system. The output costs of each process is typically the price of the reference flow and input costs of each process are known by the amount and the price of the provider flow.
In case you calculate the LCC for an ecoinvent process, make sure to copy/paste it and to remove the price from the reference product. Otherwise this price will also go into the result as a revenue.
Also check the contribution tree to see the contribution and the cost values of each input and output.
Best wishes,
Conrad