It happens when the order uses your own shipping method and the platform doesn't send us its cost. Those orders come in with zero shipping cost, and it still has to be subtracted.
Option 1: custom shipping
In the Shipping section, instead of taking the cost from the order, set up a custom cost per province, using an average where needed. This is the best option if you have a lot of orders.
Option 2: additional cost
You let the cost be taken from the order and, every time you pay your private logistics provider (every two weeks or monthly), you enter that amount as an additional fixed cost. Keep adding charges to the same cost so you don't create a new one every month.
There's one more cause people miss: if you set up a custom Tiendanube shipping method and didn't assign it a warehouse, it won't pick up the cost. Assign one and reprocess.