A change order is a way of letting the home builder know that you want to change from an original specification or selection. For example, you may want a different type of flooring material than the one specified in the contract. This will be documented in a change order and will require your signature. They could also be at a cost to the homeowner, depending on whether or not the change is within budget or not.
Changes are possible and are not by any means discouraged, however it must be understood that changes can delay the project, depending on the types of changes and at what stage of construction the changes are made.
Change orders help to eliminate the "he said, she said" as they are in writing and signed by both parties, the homeowner and home builder. Because of this, change orders are your friend and help you make sure nothing is missed.