There is a saying that good fences make for good neighbours.  We also say that good contracts make for good business relationships.  In order to avoid any confusion or ill will it is highly recommended that any changes to the project be properly discussed, negotiated and committed to writing by way of a change order.  Too often we see situations where a contractor demands payment at the end of a project for changes made by the homeowner and the prices are far more than what the homeowner anticipated. A dispute ensues and litigation sometimes follows.
Technically speaking, the contractor should be putting forward written change orders as they occur and if this is not happening the homeowner should request it or, perhaps, undertake it themselves