Inspect at every stage, and write it down
Your lender's progress inspections are not the same as your own inspection. Walk the build at each milestone with the plans and your selections list, and note everything that does not match.
One email per stage, dated, with photographs, sent to the builder and the site supervisor. It takes ten minutes and it is the single most useful thing you can do for yourself.
Keep one decision-maker and one channel
Decide who in your household approves changes, and route everything through one email thread. Two people making separate requests to a site supervisor is one of the fastest ways to blow a budget.
Handle variations in writing, before the work
A variation should say what is changing, what it costs, and how it affects the completion date. Sign it before the work happens, and keep a running total so you always know where the contract sum has moved to.
When something goes wrong
Raise it early, in writing, with the site supervisor and the builder's office. Most problems are small at that point and get expensive when they are discovered late.
If you cannot resolve it directly, your state or territory has a building disputes service that offers mediation and conciliation before anything goes to a tribunal. Check the correct body for your state and raise it there rather than letting it sit.
After the keys
Submit your defect list at practical completion, then again if anything new appears during the defects liability period. Keep the dates in writing so there is no argument about when you reported it.